Articles - 2q3m mentioned but not cited (2)
- phenix.model_vs_data: a high-level tool for the calculation of crystallographic model and data statistics. Afonine PV, Grosse-Kunstleve RW, Chen VB, Headd JJ, Moriarty NW, Richardson JS, Richardson DC, Urzhumtsev A, Zwart PH, Adams PD. J Appl Crystallogr 43 669-676 (2010)
- An unusually small dimer interface is observed in all available crystal structures of cytosolic sulfotransferases. Weitzner B, Meehan T, Xu Q, Dunbrack RL. Proteins 75 289-295 (2009)
Reviews citing this publication (19)
- Enzymes in jasmonate biosynthesis - structure, function, regulation. Schaller A, Stintzi A. Phytochemistry 70 1532-1538 (2009)
- Physiological implications of arginine metabolism in plants. Winter G, Todd CD, Trovato M, Forlani G, Funck D. Front Plant Sci 6 534 (2015)
- The glyoxalase pathway: the first hundred years... and beyond. Sousa Silva M, Gomes RA, Ferreira AE, Ponces Freire A, Cordeiro C. Biochem J 453 1-15 (2013)
- Integrative, dynamic structural biology at atomic resolution--it's about time. van den Bedem H, Fraser JS. Nat Methods 12 307-318 (2015)
- Combining experiments and simulations using the maximum entropy principle. Boomsma W, Ferkinghoff-Borg J, Lindorff-Larsen K. PLoS Comput Biol 10 e1003406 (2014)
- Visualization of macromolecular structures. O'Donoghue SI, Goodsell DS, Frangakis AS, Jossinet F, Laskowski RA, Nilges M, Saibil HR, Schafferhans A, Wade RC, Westhof E, Olson AJ. Nat Methods 7 S42-55 (2010)
- Structural dynamics, intrinsic disorder, and allostery in nuclear receptors as transcription factors. Hilser VJ, Thompson EB. J Biol Chem 286 39675-39682 (2011)
- E pluribus unum, no more: from one crystal, many conformations. Woldeyes RA, Sivak DA, Fraser JS. Curr Opin Struct Biol 28 56-62 (2014)
- Identifying and Visualizing Macromolecular Flexibility in Structural Biology. Palamini M, Canciani A, Forneris F. Front Mol Biosci 3 47 (2016)
- Molecular mechanism of enzymatic allene oxide cyclization in plants. Hofmann E, Pollmann S. Plant Physiol Biochem 46 302-308 (2008)
- Hybrid methods for macromolecular structure determination: experiment with expectations. Schröder GF. Curr Opin Struct Biol 31 20-27 (2015)
- Computational models of protein kinematics and dynamics: beyond simulation. Gipson B, Hsu D, Kavraki LE, Latombe JC. Annu Rev Anal Chem (Palo Alto Calif) 5 273-291 (2012)
- Role of Computational Methods in Going beyond X-ray Crystallography to Explore Protein Structure and Dynamics. Srivastava A, Nagai T, Srivastava A, Miyashita O, Tama F. Int J Mol Sci 19 E3401 (2018)
- Integrating Experiment and Theory to Understand TCR-pMHC Dynamics. Buckle AM, Borg NA. Front Immunol 9 2898 (2018)
- Mining electron density for functionally relevant protein polysterism in crystal structures. Fraser JS, Jackson CJ. Cell Mol Life Sci 68 1829-1841 (2011)
- Bringing diffuse X-ray scattering into focus. Wall ME, Wolff AM, Fraser JS. Curr Opin Struct Biol 50 109-116 (2018)
- Crystallographic model validation: from diagnosis to healing. Richardson JS, Prisant MG, Richardson DC. Curr Opin Struct Biol 23 707-714 (2013)
- Mapping Enzyme Landscapes by Time-Resolved Crystallography with Synchrotron and X-Ray Free Electron Laser Light. Wilson MA. Annu Rev Biophys 51 79-98 (2022)
- Hunting for predictive computational drug-discovery models. Snow CD. Expert Rev Anti Infect Ther 6 291-293 (2008)
Articles citing this publication (82)
- Alternate states of proteins revealed by detailed energy landscape mapping. Tyka MD, Keedy DA, André I, Dimaio F, Song Y, Richardson DC, Richardson JS, Baker D. J Mol Biol 405 607-618 (2011)
- The intrinsic dynamics of enzymes plays a dominant role in determining the structural changes induced upon inhibitor binding. Bakan A, Bahar I. Proc Natl Acad Sci U S A 106 14349-14354 (2009)
- Modelling dynamics in protein crystal structures by ensemble refinement. Burnley BT, Afonine PV, Adams PD, Gros P. Elife 1 e00311 (2012)
- Automated electron-density sampling reveals widespread conformational polymorphism in proteins. Lang PT, Ng HL, Fraser JS, Corn JE, Echols N, Sales M, Holton JM, Alber T. Protein Sci 19 1420-1431 (2010)
- Automated identification of functional dynamic contact networks from X-ray crystallography. van den Bedem H, Bhabha G, Yang K, Wright PE, Fraser JS. Nat Methods 10 896-902 (2013)
- Transmembrane helix uniformity examined by spectral mapping of torsion angles. Page RC, Kim S, Cross TA. Structure 16 787-797 (2008)
- Toward better refinement of comparative models: predicting loops in inexact environments. Sellers BD, Zhu K, Zhao S, Friesner RA, Jacobson MP. Proteins 72 959-971 (2008)
- Application of elastic network models to proteins in the crystalline state. Riccardi D, Cui Q, Phillips GN. Biophys J 96 464-475 (2009)
- X-ray refinement significantly underestimates the level of microscopic heterogeneity in biomolecular crystals. Kuzmanic A, Pannu NS, Zagrovic B. Nat Commun 5 3220 (2014)
- Refinement of atomic models in high resolution EM reconstructions using Flex-EM and local assessment. Joseph AP, Malhotra S, Burnley T, Wood C, Clare DK, Winn M, Topf M. Methods 100 42-49 (2016)
- Global distribution of conformational states derived from redundant models in the PDB points to non-uniqueness of the protein structure. Burra PV, Zhang Y, Godzik A, Stec B. Proc Natl Acad Sci U S A 106 10505-10510 (2009)
- Protein structural ensembles are revealed by redefining X-ray electron density noise. Lang PT, Holton JM, Fraser JS, Alber T. Proc Natl Acad Sci U S A 111 237-242 (2014)
- Comparison of apo- and heme-bound crystal structures of a truncated human heme oxygenase-2. Bianchetti CM, Yi L, Ragsdale SW, Phillips GN. J Biol Chem 282 37624-37631 (2007)
- The R-factor gap in macromolecular crystallography: an untapped potential for insights on accurate structures. Holton JM, Classen S, Frankel KA, Tainer JA. FEBS J 281 4046-4060 (2014)
- Systematic comparison of crystal and NMR protein structures deposited in the protein data bank. Sikic K, Tomic S, Carugo O. Open Biochem J 4 83-95 (2010)
- A Multi-model Approach to Assessing Local and Global Cryo-EM Map Quality. Herzik MA, Fraser JS, Lander GC. Structure 27 344-358.e3 (2019)
- Protein similarity networks reveal relationships among sequence, structure, and function within the Cupin superfamily. Uberto R, Moomaw EW. PLoS One 8 e74477 (2013)
- Molecular dynamics simulation of triclinic lysozyme in a crystal lattice. Janowski PA, Liu C, Deckman J, Case DA. Protein Sci 25 87-102 (2016)
- Similarity measures for protein ensembles. Lindorff-Larsen K, Ferkinghoff-Borg J. PLoS One 4 e4203 (2009)
- qFit-ligand Reveals Widespread Conformational Heterogeneity of Drug-Like Molecules in X-Ray Electron Density Maps. van Zundert GCP, Hudson BM, de Oliveira SHP, Keedy DA, Fonseca R, Heliou A, Suresh P, Borrelli K, Day T, Fraser JS, van den Bedem H. J Med Chem 61 11183-11198 (2018)
- Flexible backbone sampling methods to model and design protein alternative conformations. Ollikainen N, Smith CA, Fraser JS, Kortemme T. Methods Enzymol 523 61-85 (2013)
- A stable antimicrobial peptide with dual functions of treating and preventing citrus Huanglongbing. Huang CY, Araujo K, Sánchez JN, Kund G, Trumble J, Roper C, Godfrey KE, Jin H. Proc Natl Acad Sci U S A 118 e2019628118 (2021)
- Active site and laminarin binding in glycoside hydrolase family 55. Bianchetti CM, Takasuka TE, Deutsch S, Udell HS, Yik EJ, Bergeman LF, Fox BG. J Biol Chem 290 11819-11832 (2015)
- TLS from fundamentals to practice. Urzhumtsev A, Afonine PV, Adams PD. Crystallogr Rev 19 230-270 (2013)
- Molecular dynamics simulation and molecular docking studies of Angiotensin converting enzyme with inhibitor lisinopril and amyloid Beta Peptide. Jalkute CB, Barage SH, Dhanavade MJ, Sonawane KD. Protein J 32 356-364 (2013)
- Structural and functional characterization of Salmonella enterica serovar Typhimurium YcbL: an unusual Type II glyoxalase. Stamp AL, Owen P, El Omari K, Nichols CE, Lockyer M, Lamb HK, Charles IG, Hawkins AR, Stammers DK. Protein Sci 19 1897-1905 (2010)
- The Center for Eukaryotic Structural Genomics. Markley JL, Aceti DJ, Bingman CA, Fox BG, Frederick RO, Makino S, Nichols KW, Phillips GN, Primm JG, Sahu SC, Vojtik FC, Volkman BF, Wrobel RL, Zolnai Z. J Struct Funct Genomics 10 165-179 (2009)
- Comparisons of experimental and computed protein anisotropic temperature factors. Yang L, Song G, Jernigan RL. Proteins 76 164-175 (2009)
- Protein structure along the order-disorder continuum. Fisher CK, Stultz CM. J Am Chem Soc 133 10022-10025 (2011)
- Efficient algorithms to explore conformation spaces of flexible protein loops. Yao P, Dhanik A, Marz N, Propper R, Kou C, Liu G, van den Bedem H, Latombe JC, Halperin-Landsberg I, Altman RB. IEEE/ACM Trans Comput Biol Bioinform 5 534-545 (2008)
- Biochemical phenotype of a common disease-causing mutation and a possible therapeutic approach for the phosphomannomutase 2-associated disorder of glycosylation. Andreotti G, Pedone E, Giordano A, Cubellis MV. Mol Genet Genomic Med 1 32-44 (2013)
- Salvage of the thiamin pyrimidine moiety by plant TenA proteins lacking an active-site cysteine. Zallot R, Yazdani M, Goyer A, Ziemak MJ, Guan JC, McCarty DR, de Crécy-Lagard V, Gerdes S, Garrett TJ, Benach J, Hunt JF, Shintani DK, Hanson AD. Biochem J 463 145-155 (2014)
- Transmembrane helix orientation and dynamics: insights from ensemble dynamics with solid-state NMR observables. Jo S, Im W. Biophys J 100 2913-2921 (2011)
- Evidence of functional protein dynamics from X-ray crystallographic ensembles. Kohn JE, Afonine PV, Ruscio JZ, Adams PD, Head-Gordon T. PLoS Comput Biol 6 e1000911 (2010)
- Ensemble MD simulations restrained via crystallographic data: accurate structure leads to accurate dynamics. Xue Y, Skrynnikov NR. Protein Sci 23 488-507 (2014)
- Insights into the structure and function of fungal β-mannosidases from glycoside hydrolase family 2 based on multiple crystal structures of the Trichoderma harzianum enzyme. Nascimento AS, Muniz JR, Aparício R, Golubev AM, Polikarpov I. FEBS J 281 4165-4178 (2014)
- Mercaptosuccinate dioxygenase, a cysteine dioxygenase homologue, from Variovorax paradoxus strain B4 is the key enzyme of mercaptosuccinate degradation. Brandt U, Schürmann M, Steinbüchel A. J Biol Chem 289 30800-30809 (2014)
- Modeling of Protein⁻Protein Interactions in Cytokinin Signal Transduction. Arkhipov DV, Lomin SN, Myakushina YA, Savelieva EM, Osolodkin DI, Romanov GA. Int J Mol Sci 20 E2096 (2019)
- Activity Regulation by Heteromerization of Arabidopsis Allene Oxide Cyclase Family Members. Otto M, Naumann C, Brandt W, Wasternack C, Hause B. Plants (Basel) 5 E3 (2016)
- A comparative analysis of the equilibrium dynamics of a designed protein inferred from NMR, X-ray, and computations. Liu L, Koharudin LM, Gronenborn AM, Bahar I. Proteins 77 927-939 (2009)
- Auxin amidohydrolases from Brassica rapa cleave the alanine conjugate of indolepropionic acid as a preferable substrate: a biochemical and modeling approach. Savić B, Tomić S, Magnus V, Gruden K, Barle K, Grenković R, Ludwig-Müller J, Salopek-Sondi B. Plant Cell Physiol 50 1587-1599 (2009)
- Probing protein ensemble rigidity and hydrogen-deuterium exchange. Sljoka A, Wilson D. Phys Biol 10 056013 (2013)
- The 2/2 hemoglobin from the cyanobacterium Synechococcus sp. PCC 7002 with covalently attached heme: comparison of X-ray and NMR structures. Wenke BB, Lecomte JT, Héroux A, Schlessman JL. Proteins 82 528-534 (2014)
- Evolution of the key alkaloid enzyme putrescine N-methyltransferase from spermidine synthase. Junker A, Fischer J, Sichhart Y, Brandt W, Dräger B. Front Plant Sci 4 260 (2013)
- Percentile-based spread: a more accurate way to compare crystallographic models. Pozharski E. Acta Crystallogr D Biol Crystallogr 66 970-978 (2010)
- Medicago truncatula histidine-containing phosphotransfer protein: structural and biochemical insights into the cytokinin transduction pathway in plants. Ruszkowski M, Brzezinski K, Jedrzejczak R, Dauter M, Dauter Z, Sikorski M, Jaskolski M. FEBS J 280 3709-3720 (2013)
- Multistart simulated annealing refinement of the crystal structure of the 70S ribosome. Korostelev A, Laurberg M, Noller HF. Proc Natl Acad Sci U S A 106 18195-18200 (2009)
- Promiscuous metallo-β-lactamases: MIM-1 and MIM-2 may play an essential role in quorum sensing networks. Miraula M, Schenk G, Mitić N. J Inorg Biochem 162 366-375 (2016)
- Solution structure of an ultra-stable single-chain insulin analog connects protein dynamics to a novel mechanism of receptor binding. Glidden MD, Yang Y, Smith NA, Phillips NB, Carr K, Wickramasinghe NP, Ismail-Beigi F, Lawrence MC, Smith BJ, Weiss MA. J Biol Chem 293 69-88 (2018)
- Stable calcium-free myocilin olfactomedin domain variants reveal challenges in differentiating between benign and glaucoma-causing mutations. Hill SE, Kwon MS, Martin MD, Suntharalingam A, Hazel A, Dickey CA, Gumbart JC, Lieberman RL. J Biol Chem 294 12717-12728 (2019)
- Identifying proteins that can form tyrosine-cysteine crosslinks. Martinie RJ, Godakumbura PI, Porter EG, Divakaran A, Burkhart BJ, Wertz JT, Benson DE. Metallomics 4 1037-42, 1008 (2012)
- Forging tools for refining predicted protein structures. Lin X, Schafer NP, Lu W, Jin S, Chen X, Chen M, Onuchic JN, Wolynes PG. Proc Natl Acad Sci U S A 116 9400-9409 (2019)
- Structural variability and the incoherent addition of scattered intensities in single-particle diffraction. Maia FR, Ekeberg T, Tîmneanu N, van der Spoel D, Hajdu J. Phys Rev E Stat Nonlin Soft Matter Phys 80 031905 (2009)
- Structure of TTHA1623, a novel metallo-beta-lactamase superfamily protein from Thermus thermophilus HB8. Yamamura A, Okada A, Kameda Y, Ohtsuka J, Nakagawa N, Ebihara A, Nagata K, Tanokura M. Acta Crystallogr Sect F Struct Biol Cryst Commun 65 455-459 (2009)
- Residue-level global and local ensemble-ensemble comparisons of protein domains. Clark SA, Tronrud DE, Karplus PA. Protein Sci 24 1528-1542 (2015)
- Describing protein conformational ensembles: beyond static snapshots. Phillips GN. F1000 Biol Rep 1 38 (2009)
- Enhancing the quality of protein conformation ensembles with relative populations. Vammi V, Lin TL, Song G. J Biomol NMR 58 209-225 (2014)
- Hybrid Refinement of Heterogeneous Conformational Ensembles Using Spectroscopic Data. Hays JM, Cafiso DS, Kasson PM. J Phys Chem Lett 10 3410-3414 (2019)
- Refinement of Highly Flexible Protein Structures using Simulation-Guided Spectroscopy. Hays JM, Kieber MK, Li JZ, Han JI, Columbus L, Kasson PM. Angew Chem Int Ed Engl 57 17110-17114 (2018)
- The maximum penalty criterion for ridge regression: application to the calibration of the force constant in elastic network models. Dehouck Y, Bastolla U. Integr Biol (Camb) 9 627-641 (2017)
- Conformational Plasticity of HLA-B27 Molecules Correlates Inversely With Efficiency of Negative T Cell Selection. Loll B, Rückert C, Uchanska-Ziegler B, Ziegler A. Front Immunol 11 179 (2020)
- Liquid-like and rigid-body motions in molecular-dynamics simulations of a crystalline protein. Wych DC, Fraser JS, Mobley DL, Wall ME. Struct Dyn 6 064704 (2019)
- The 3-His Metal Coordination Site Promotes the Coupling of Oxygen Activation to Cysteine Oxidation in Cysteine Dioxygenase. Forbes DL, Meneely KM, Chilton AS, Lamb AL, Ellis HR. Biochemistry 59 2022-2031 (2020)
- The role of conserved Cys residues in Brassica rapa auxin amidohydrolase: Cys139 is crucial for the enzyme activity and Cys320 regulates enzyme stability. Smolko A, Šupljika F, Martinčić J, Jajčanin-Jozić N, Grabar-Branilović M, Tomić S, Ludwig-Müller J, Piantanida I, Salopek-Sondi B. Phys Chem Chem Phys 18 8890-8900 (2016)
- 3D Domain Swapping Dimerization of the Receiver Domain of Cytokinin Receptor CRE1 From Arabidopsis thaliana and Medicago truncatula. Tran LH, Urbanowicz A, Jasiński M, Jaskolski M, Ruszkowski M. Front Plant Sci 12 756341 (2021)
- Citrullination of Proteins as a Specific Response Mechanism in Plants. Marondedze C, Elia G, Thomas L, Wong A, Gehring C. Front Plant Sci 12 638392 (2021)
- Impact of HLA-DR Antigen Binding Cleft Rigidity on T Cell Recognition. Szeto C, Bloom JI, Sloane H, Lobos CA, Fodor J, Jayasinghe D, Chatzileontiadou DSM, Grant EJ, Buckle AM, Gras S. Int J Mol Sci 21 E7081 (2020)
- Loop dynamics of thymidine diphosphate-rhamnose 3'-O-methyltransferase (CalS11), an enzyme in calicheamicin biosynthesis. Han L, Singh S, Thorson JS, Phillips GN. Struct Dyn 3 012004 (2016)
- New insight into the dynamic properties and the active site architecture of H-Ras p21 revealed by X-ray crystallography at very high resolution. Klink BU, Scheidig AJ. BMC Struct Biol 10 38 (2010)
- Structural dynamics of a methionine γ-lyase for calicheamicin biosynthesis: Rotation of the conserved tyrosine stacking with pyridoxal phosphate. Cao H, Tan K, Wang F, Bigelow L, Yennamalli RM, Jedrzejczak R, Babnigg G, Bingman CA, Joachimiak A, Kharel MK, Singh S, Thorson JS, Phillips GN. Struct Dyn 3 034702 (2016)
- Structure of a cupin protein Plu4264 from Photorhabdus luminescens subsp. laumondii TTO1 at 1.35 Å resolution. Weerth RS, Michalska K, Bingman CA, Yennamalli RM, Li H, Jedrzejczak R, Wang F, Babnigg G, Joachimiak A, Thomas MG, Phillips GN. Proteins 83 383-388 (2015)
- Dual Activity BLEG-1 from Bacillus lehensis G1 Revealed Structural Resemblance to B3 Metallo-β-Lactamase and Glyoxalase II: An Insight into Its Enzyme Promiscuity and Evolutionary Divergence. Au SX, Dzulkifly NS, Muhd Noor ND, Matsumura H, Raja Abdul Rahman RNZ, Normi YM. Int J Mol Sci 22 9377 (2021)
- Engineering a new-to-nature cascade for phosphate-dependent formate to formaldehyde conversion in vitro and in vivo. Nattermann M, Wenk S, Pfister P, He H, Lee SH, Szymanski W, Guntermann N, Zhu F, Nickel L, Wallner C, Zarzycki J, Paczia N, Gaißert N, Franciò G, Leitner W, Gonzalez R, Erb TJ. Nat Commun 14 2682 (2023)
- Interactions that know no boundaries. Wall ME. IUCrJ 5 120-121 (2018)
- Molecular-dynamics simulation methods for macromolecular crystallography. Wych DC, Aoto PC, Vu L, Wolff AM, Mobley DL, Fraser JS, Taylor SS, Wall ME. Acta Crystallogr D Struct Biol 79 50-65 (2023)
- Protein crystal lattices are dynamic assemblies: the role of conformational entropy in the protein condensed phase. Dimova M, Devedjiev YD. IUCrJ 5 130-140 (2018)
- Capturing the Dynamics of a Spring-Loaded Protein. Mitchell JA, O'Mara ML. Structure 25 963-964 (2017)
- FLEXR: automated multi-conformer model building using electron-density map sampling. Stachowski TR, Fischer M. Acta Crystallogr D Struct Biol 79 354-367 (2023)
- Modeling a unit cell: crystallographic refinement procedure using the biomolecular MD simulation platform Amber. Mikhailovskii O, Xue Y, Skrynnikov NR. IUCrJ 9 114-133 (2022)
- PDB-NMA of a protein homodimer reproduces distinct experimental motility asymmetry. Tirion MM, Ben-Avraham D. Phys Biol 15 026004 (2018)
- Simultaneous use of solution, solid-state NMR and X-ray crystallography to study the conformational landscape of the Crh protein during oligomerization and crystallization. Bardiaux B, Favier A, Etzkorn M, Baldus M, Böckmann A, Nilges M, Malliavin TE. Adv Appl Bioinform Chem 3 25-38 (2010)
- Synergism between x-ray crystallography and NMR residual dipolar couplings in characterizing protein dynamics. Shen Y, Bax A. Struct Dyn 10 040901 (2023)
Related citations provided by authors (1)
- Crystal structure of At2g03760, a putative steroid sulfotransferase from Arabidopsis thaliana.. Smith DW, Johnson KA, Bingman CA, Aceti DJ, Blommel PG, Wrobel RL, Frederick RO, Zhao Q, Sreenath H, Fox BG, Volkman BF, Jeon WB, Newman CS, Ulrich EL, Hegeman AD, Kimball T, Thao S, Sussman MR, Markley JL, Phillips GN Proteins 57 854-7 (2004)