HEADER PROTEIN FIBRIL 05-AUG-22 8ANI TITLE STRUCTURE OF THE AMYLOID-FORMING PEPTIDE LYIQWL FROM TC5B, GROWN FROM TITLE 2 10% ETHANOL COMPND MOL_ID: 1; COMPND 2 MOLECULE: PEPTIDE LYIQWL FROM TC5B; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 4 ORGANISM_TAXID: 32630 KEYWDS AMYLOID, PROTEIN FIBRIL EXPDTA X-RAY DIFFRACTION AUTHOR Z.DURVANGER REVDAT 2 09-AUG-23 8ANI 1 JRNL REVDAT 1 02-AUG-23 8ANI 0 JRNL AUTH D.HORVATH,Z.DURVANGER,D.K MENYHARD,M.SULYOK-EILER,F.BENCS, JRNL AUTH 2 G.GYULAI,P.HORVATH,N.TARICSKA,A.PERCZEL JRNL TITL POLYMORPHIC AMYLOID NANOSTRUCTURES OF HORMONE PEPTIDES JRNL TITL 2 INVOLVED IN GLUCOSE HOMEOSTASIS DISPLAY REVERSIBLE AMYLOID JRNL TITL 3 FORMATION. JRNL REF NAT COMMUN V. 14 4621 2023 JRNL REFN ESSN 2041-1723 JRNL PMID 37528104 JRNL DOI 10.1038/S41467-023-40294-X REMARK 2 REMARK 2 RESOLUTION. 1.35 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.20.1_4487 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.35 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 18.76 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.380 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.7 REMARK 3 NUMBER OF REFLECTIONS : 2244 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.118 REMARK 3 R VALUE (WORKING SET) : 0.114 REMARK 3 FREE R VALUE : 0.152 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.850 REMARK 3 FREE R VALUE TEST SET COUNT : 221 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 18.7600 - 1.7000 0.99 1028 111 0.1013 0.1279 REMARK 3 2 1.7000 - 1.3500 0.96 995 110 0.1433 0.2064 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.099 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 8.642 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 5.60 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 5.95 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.013 150 REMARK 3 ANGLE : 1.410 202 REMARK 3 CHIRALITY : 0.111 20 REMARK 3 PLANARITY : 0.009 21 REMARK 3 DIHEDRAL : 14.974 45 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): -0.6076 0.8080 1.7978 REMARK 3 T TENSOR REMARK 3 T11: 0.0288 T22: 0.0502 REMARK 3 T33: 0.0390 T12: 0.0020 REMARK 3 T13: -0.0116 T23: 0.0036 REMARK 3 L TENSOR REMARK 3 L11: 0.9153 L22: 1.1294 REMARK 3 L33: 1.6786 L12: -0.0944 REMARK 3 L13: -0.3316 L23: 0.7929 REMARK 3 S TENSOR REMARK 3 S11: 0.0126 S12: -0.0060 S13: -0.0133 REMARK 3 S21: -0.0364 S22: 0.0099 S23: 0.0076 REMARK 3 S31: -0.0217 S32: -0.0325 S33: -0.0242 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 8ANI COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 11-AUG-22. REMARK 100 THE DEPOSITION ID IS D_1292124821. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 26-JAN-22 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU PHOTONJET-R REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54184 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : RIGAKU HYPIX-6000HE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : CRYSALISPRO REMARK 200 DATA SCALING SOFTWARE : CRYSALISPRO REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 2253 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.350 REMARK 200 RESOLUTION RANGE LOW (A) : 18.760 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.1 REMARK 200 DATA REDUNDANCY : 4.930 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 7.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.35 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.40 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.200 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: CRYSTAL STRUCTURE OF LYIQWL GROWN FROM REMARK 200 ACETONITRILE/WATER REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 20.38 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.54 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEPTIDE WAS DISSOLVED IN 10% ETHANOL REMARK 280 AT 0.5 MG/ML CONCENTRATION, THEN INCUBATED AT 293K OVERNIGHT., REMARK 280 EVAPORATION, RECRYSTALLIZATION REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 11.73350 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 DBREF 8ANI A 1 6 PDB 8ANI 8ANI 1 6 DBREF 8ANI B 1 6 PDB 8ANI 8ANI 1 6 SEQRES 1 A 6 LEU TYR ILE GLN TRP LEU SEQRES 1 B 6 LEU TYR ILE GLN TRP LEU HET TFA B 101 14 HET EOH B 102 9 HET EOH B 103 18 HETNAM TFA TRIFLUOROACETIC ACID HETNAM EOH ETHANOL FORMUL 3 TFA C2 H F3 O2 FORMUL 4 EOH 2(C2 H6 O) FORMUL 6 HOH *3(H2 O) SHEET 1 AA1 2 TYR A 2 TRP A 5 0 SHEET 2 AA1 2 TYR B 2 TRP B 5 -1 O GLN B 4 N ILE A 3 CRYST1 11.719 23.467 18.762 90.00 90.04 90.00 P 1 21 1 4 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.085332 0.000000 0.000060 0.00000 SCALE2 0.000000 0.042613 0.000000 0.00000 SCALE3 0.000000 0.000000 0.053299 0.00000