HEADER DNA BINDING PROTEIN 24-FEB-23 8IIN TITLE COMPLEX FORM OF MSMUDGX H109K MUTANT AND URACIL- OBTAINED FROM URACIL TITLE 2 DNA (TTUTT) POST ITS CLEAVAGE BY MSMUDGX H109K COMPND MOL_ID: 1; COMPND 2 MOLECULE: TYPE-4 URACIL-DNA GLYCOSYLASE; COMPND 3 CHAIN: A; COMPND 4 EC: 3.2.2.27; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MYCOLICIBACTERIUM SMEGMATIS MC2 155; SOURCE 3 ORGANISM_TAXID: 246196; SOURCE 4 STRAIN: MC2 155; SOURCE 5 ATCC: 700084; SOURCE 6 GENE: MSMEG_0265; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 9 EXPRESSION_SYSTEM_VARIANT: ROSETTA; SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PET14B KEYWDS UDGX, H109K, URACIL, COMPLEX, PROTEIN, DNA BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR S.AROLI REVDAT 3 29-MAY-24 8IIN 1 REMARK REVDAT 2 02-AUG-23 8IIN 1 JRNL REVDAT 1 21-JUN-23 8IIN 0 JRNL AUTH S.AROLI,E.J.WOO,B.GOPAL,U.VARSHNEY JRNL TITL MUTATIONAL AND STRUCTURAL ANALYSES OF UDGX: INSIGHTS INTO JRNL TITL 2 THE ACTIVE SITE POCKET ARCHITECTURE AND ITS EVOLUTION. JRNL REF NUCLEIC ACIDS RES. V. 51 6554 2023 JRNL REFN ESSN 1362-4962 JRNL PMID 37283083 JRNL DOI 10.1093/NAR/GKAD486 REMARK 2 REMARK 2 RESOLUTION. 1.61 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.2 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 : MLHL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.61 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 23.59 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.950 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.9 REMARK 3 NUMBER OF REFLECTIONS : 24565 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.163 REMARK 3 R VALUE (WORKING SET) : 0.162 REMARK 3 FREE R VALUE : 0.183 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.840 REMARK 3 FREE R VALUE TEST SET COUNT : 1188 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 23.5900 - 3.2200 0.99 3088 161 0.1577 0.1770 REMARK 3 2 3.2200 - 2.5500 0.98 3024 147 0.1595 0.1744 REMARK 3 3 2.5500 - 2.2300 0.97 2964 148 0.1574 0.1855 REMARK 3 4 2.2300 - 2.0300 0.97 2913 165 0.1566 0.1757 REMARK 3 5 2.0300 - 1.8800 0.95 2909 155 0.1527 0.1733 REMARK 3 6 1.8800 - 1.7700 0.95 2896 130 0.1658 0.1982 REMARK 3 7 1.7700 - 1.6800 0.93 2822 137 0.1780 0.2210 REMARK 3 8 1.6800 - 1.6100 0.92 2761 145 0.2153 0.2386 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) : 0.110 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 17.480 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 : 0.006 1612 REMARK 3 ANGLE : 0.949 2187 REMARK 3 CHIRALITY : 0.067 248 REMARK 3 PLANARITY : 0.008 289 REMARK 3 DIHEDRAL : 6.488 231 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL 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 8IIN COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 09-MAR-23. REMARK 100 THE DEPOSITION ID IS D_1300035747. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-APR-21 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.8-7.2 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 : BRUKER AXS MICROSTAR REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54179 REMARK 200 MONOCHROMATOR : M REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MAR SCANNER 345 MM PLATE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : IMOSFLM REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 24583 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.600 REMARK 200 RESOLUTION RANGE LOW (A) : 28.120 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.0 REMARK 200 DATA REDUNDANCY : 4.900 REMARK 200 R MERGE (I) : 0.06400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.63 REMARK 200 COMPLETENESS FOR SHELL (%) : 66.6 REMARK 200 DATA REDUNDANCY IN SHELL : 4.40 REMARK 200 R MERGE FOR SHELL (I) : 0.56800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.900 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.20 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.29 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2.0M AMMONIUM CITRATE TRIBASIC PH7.0, REMARK 280 0.1M BIS-TRIS PROPANE PH7.0, MICROBATCH, TEMPERATURE 295K 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 25.77000 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 380 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 9670 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -20.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A 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 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 GLU A 23 OE2 REMARK 470 ARG A 31 NH1 REMARK 470 ASP A 85 CG OD1 OD2 REMARK 470 LYS A 105 CG CD CE NZ REMARK 470 ARG A 106 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 110 CD CE NZ REMARK 470 ASP A 166 CG OD1 OD2 REMARK 470 ARG A 184 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 187 CG CD CE NZ REMARK 470 GLU A 189 OE1 REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SF4 A 301 FE3 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 24 SG REMARK 620 2 SF4 A 301 S1 120.0 REMARK 620 3 SF4 A 301 S2 107.1 106.4 REMARK 620 4 SF4 A 301 S4 113.6 102.4 106.4 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SF4 A 301 FE2 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 27 SG REMARK 620 2 SF4 A 301 S1 118.2 REMARK 620 3 SF4 A 301 S3 99.9 106.7 REMARK 620 4 SF4 A 301 S4 120.8 104.1 105.6 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SF4 A 301 FE4 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 95 ND1 REMARK 620 2 SF4 A 301 S1 108.0 REMARK 620 3 SF4 A 301 S2 108.6 105.8 REMARK 620 4 SF4 A 301 S3 122.3 106.9 104.1 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SF4 A 301 FE1 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 120 SG REMARK 620 2 SF4 A 301 S2 115.4 REMARK 620 3 SF4 A 301 S3 113.4 104.9 REMARK 620 4 SF4 A 301 S4 110.3 106.8 105.2 REMARK 620 N 1 2 3 DBREF 8IIN A 2 207 UNP A0QP43 A0QP43_MYCS2 2 207 SEQADV 8IIN LYS A 109 UNP A0QP43 HIS 109 ENGINEERED MUTATION SEQRES 1 A 206 ALA GLY ALA GLN ASP PHE VAL PRO HIS THR ALA ASP LEU SEQRES 2 A 206 ALA GLU LEU ALA ALA ALA ALA GLY GLU CYS ARG GLY CYS SEQRES 3 A 206 GLY LEU TYR ARG ASP ALA THR GLN ALA VAL PHE GLY ALA SEQRES 4 A 206 GLY GLY ARG SER ALA ARG ILE MET MET ILE GLY GLU GLN SEQRES 5 A 206 PRO GLY ASP LYS GLU ASP LEU ALA GLY LEU PRO PHE VAL SEQRES 6 A 206 GLY PRO ALA GLY ARG LEU LEU ASP ARG ALA LEU GLU ALA SEQRES 7 A 206 ALA ASP ILE ASP ARG ASP ALA LEU TYR VAL THR ASN ALA SEQRES 8 A 206 VAL LYS HIS PHE LYS PHE THR ARG ALA ALA GLY GLY LYS SEQRES 9 A 206 ARG ARG ILE LYS LYS THR PRO SER ARG THR GLU VAL VAL SEQRES 10 A 206 ALA CYS ARG PRO TRP LEU ILE ALA GLU MET THR SER VAL SEQRES 11 A 206 GLU PRO ASP VAL VAL VAL LEU LEU GLY ALA THR ALA ALA SEQRES 12 A 206 LYS ALA LEU LEU GLY ASN ASP PHE ARG VAL THR GLN HIS SEQRES 13 A 206 ARG GLY GLU VAL LEU HIS VAL ASP ASP VAL PRO GLY ASP SEQRES 14 A 206 PRO ALA LEU VAL ALA THR VAL HIS PRO SER SER LEU LEU SEQRES 15 A 206 ARG GLY PRO LYS GLU GLU ARG GLU SER ALA PHE ALA GLY SEQRES 16 A 206 LEU VAL ASP ASP LEU ARG VAL ALA ALA ASP VAL HET SF4 A 301 8 HET URA A 302 8 HETNAM SF4 IRON/SULFUR CLUSTER HETNAM URA URACIL FORMUL 2 SF4 FE4 S4 FORMUL 3 URA C4 H4 N2 O2 FORMUL 4 HOH *166(H2 O) HELIX 1 AA1 ALA A 4 VAL A 8 5 5 HELIX 2 AA2 ASP A 13 GLY A 22 1 10 HELIX 3 AA3 CYS A 27 ARG A 31 5 5 HELIX 4 AA4 GLY A 55 GLY A 62 1 8 HELIX 5 AA5 GLY A 67 ALA A 80 1 14 HELIX 6 AA6 ASP A 83 ASP A 85 5 3 HELIX 7 AA7 SER A 113 GLU A 132 1 20 HELIX 8 AA8 GLY A 140 GLY A 149 1 10 HELIX 9 AA9 ARG A 153 HIS A 157 5 5 HELIX 10 AB1 HIS A 178 LEU A 183 5 6 HELIX 11 AB2 PRO A 186 ASP A 206 1 21 SHEET 1 AA1 4 LEU A 87 ASN A 91 0 SHEET 2 AA1 4 ILE A 47 GLY A 51 1 N MET A 49 O THR A 90 SHEET 3 AA1 4 VAL A 135 LEU A 139 1 O VAL A 137 N MET A 48 SHEET 4 AA1 4 ALA A 172 THR A 176 1 O THR A 176 N LEU A 138 SHEET 1 AA2 2 PHE A 98 THR A 99 0 SHEET 2 AA2 2 ILE A 108 LYS A 109 -1 O ILE A 108 N THR A 99 LINK SG CYS A 24 FE3 SF4 A 301 1555 1555 2.31 LINK SG CYS A 27 FE2 SF4 A 301 1555 1555 2.33 LINK ND1 HIS A 95 FE4 SF4 A 301 1555 1555 2.35 LINK SG CYS A 120 FE1 SF4 A 301 1555 1555 2.31 CRYST1 36.460 51.540 54.860 90.00 104.71 90.00 P 1 21 1 2 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 0.027427 0.000000 0.007201 0.00000 SCALE2 0.000000 0.019402 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018846 0.00000