HEADER DNA BINDING PROTEIN 28-AUG-18 6AJS TITLE H109S MUTANT FORM OF URACIL DNA GLYCOSYLASE X. COMPND MOL_ID: 1; COMPND 2 MOLECULE: URACIL DNA GLYCOSYLASE SUPERFAMILY PROTEIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MYCOBACTERIUM SMEGMATIS MC2 155; SOURCE 3 ORGANISM_TAXID: 246196; SOURCE 4 STRAIN: MC2 155; SOURCE 5 GENE: MSMEG_0265; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) KEYWDS DNA REPAIR, BASE EXCISION, DNA-PROTEIN CROSSLINK., DNA BINDING KEYWDS 2 PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR W.C.AHN,S.AROLI,U.VARSHNEY,E.J.WOO REVDAT 2 27-MAR-24 6AJS 1 REMARK REVDAT 1 29-MAY-19 6AJS 0 JRNL AUTH W.C.AHN,S.AROLI,J.H.KIM,J.H.MOON,G.S.LEE,M.H.LEE,P.B.SANG, JRNL AUTH 2 B.H.OH,U.VARSHNEY,E.J.WOO JRNL TITL COVALENT BINDING OF URACIL DNA GLYCOSYLASE UDGX TO ABASIC JRNL TITL 2 DNA UPON URACIL EXCISION. JRNL REF NAT.CHEM.BIOL. V. 15 607 2019 JRNL REFN ESSN 1552-4469 JRNL PMID 31101917 JRNL DOI 10.1038/S41589-019-0289-3 REMARK 2 REMARK 2 RESOLUTION. 1.63 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.12_2829: ???) 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.63 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.02 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.0 REMARK 3 NUMBER OF REFLECTIONS : 23412 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) : 0.160 REMARK 3 FREE R VALUE : 0.197 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 8.560 REMARK 3 FREE R VALUE TEST SET COUNT : 2003 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 28.0266 - 3.9298 0.79 1287 119 0.1895 0.2090 REMARK 3 2 3.9298 - 3.1206 0.96 1538 146 0.1565 0.1870 REMARK 3 3 3.1206 - 2.7265 0.99 1557 140 0.1697 0.1917 REMARK 3 4 2.7265 - 2.4774 1.00 1562 153 0.1641 0.2068 REMARK 3 5 2.4774 - 2.2999 1.00 1594 143 0.1565 0.2128 REMARK 3 6 2.2999 - 2.1643 0.99 1554 147 0.1521 0.1897 REMARK 3 7 2.1643 - 2.0560 0.99 1560 148 0.1494 0.1877 REMARK 3 8 2.0560 - 1.9665 1.00 1536 151 0.1467 0.1836 REMARK 3 9 1.9665 - 1.8908 1.00 1598 141 0.1454 0.2037 REMARK 3 10 1.8908 - 1.8256 1.00 1530 155 0.1437 0.2041 REMARK 3 11 1.8256 - 1.7685 1.00 1603 131 0.1447 0.1861 REMARK 3 12 1.7685 - 1.7180 1.00 1545 162 0.1415 0.2036 REMARK 3 13 1.7180 - 1.6727 1.00 1560 146 0.1436 0.1940 REMARK 3 14 1.6727 - 1.6319 0.88 1385 121 0.1447 0.1926 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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) : 0.130 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 17.380 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 : 0.007 1576 REMARK 3 ANGLE : 0.937 2145 REMARK 3 CHIRALITY : 0.060 242 REMARK 3 PLANARITY : 0.006 285 REMARK 3 DIHEDRAL : 10.513 952 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 6AJS COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 07-SEP-18. REMARK 100 THE DEPOSITION ID IS D_1300008836. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 19-MAY-16 REMARK 200 TEMPERATURE (KELVIN) : 190 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PAL/PLS REMARK 200 BEAMLINE : 7A (6B, 6C1) REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.987 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 270 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 23431 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.630 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.4 REMARK 200 DATA REDUNDANCY : 6.200 REMARK 200 R MERGE (I) : 0.06300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 56.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.63 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.66 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.12900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MIR REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.30 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.21 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2.0M AMMONIUM CITRATE TRIBASIC PH7.0, REMARK 280 0.1M BIS-TRIS PROPANE PH7.0, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 290K 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 25.69650 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: 10070 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 MET A 1 REMARK 465 PRO A 209 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O ALA A 86 O HOH A 401 2.04 REMARK 500 O HOH A 555 O HOH A 557 2.04 REMARK 500 O HOH A 580 O HOH A 598 2.12 REMARK 500 O HOH A 453 O HOH A 596 2.15 REMARK 500 NE ARG A 106 O HOH A 402 2.17 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 594 O HOH A 608 2454 2.11 REMARK 500 REMARK 500 REMARK: NULL 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 120.6 REMARK 620 3 SF4 A 301 S2 104.6 107.1 REMARK 620 4 SF4 A 301 S4 114.3 102.4 107.1 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 117.2 REMARK 620 3 SF4 A 301 S3 102.0 107.9 REMARK 620 4 SF4 A 301 S4 120.2 102.6 106.1 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 106.3 REMARK 620 3 SF4 A 301 S2 107.0 106.9 REMARK 620 4 SF4 A 301 S3 123.3 108.1 104.3 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 113.5 REMARK 620 3 SF4 A 301 S3 113.8 104.4 REMARK 620 4 SF4 A 301 S4 112.1 106.4 105.9 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SF4 A 301 DBREF 6AJS A 1 209 UNP A0QP43 A0QP43_MYCS2 1 209 SEQADV 6AJS SER A 109 UNP A0QP43 HIS 109 ENGINEERED MUTATION SEQRES 1 A 209 MET ALA GLY ALA GLN ASP PHE VAL PRO HIS THR ALA ASP SEQRES 2 A 209 LEU ALA GLU LEU ALA ALA ALA ALA GLY GLU CYS ARG GLY SEQRES 3 A 209 CYS GLY LEU TYR ARG ASP ALA THR GLN ALA VAL PHE GLY SEQRES 4 A 209 ALA GLY GLY ARG SER ALA ARG ILE MET MET ILE GLY GLU SEQRES 5 A 209 GLN PRO GLY ASP LYS GLU ASP LEU ALA GLY LEU PRO PHE SEQRES 6 A 209 VAL GLY PRO ALA GLY ARG LEU LEU ASP ARG ALA LEU GLU SEQRES 7 A 209 ALA ALA ASP ILE ASP ARG ASP ALA LEU TYR VAL THR ASN SEQRES 8 A 209 ALA VAL LYS HIS PHE LYS PHE THR ARG ALA ALA GLY GLY SEQRES 9 A 209 LYS ARG ARG ILE SER LYS THR PRO SER ARG THR GLU VAL SEQRES 10 A 209 VAL ALA CYS ARG PRO TRP LEU ILE ALA GLU MET THR SER SEQRES 11 A 209 VAL GLU PRO ASP VAL VAL VAL LEU LEU GLY ALA THR ALA SEQRES 12 A 209 ALA LYS ALA LEU LEU GLY ASN ASP PHE ARG VAL THR GLN SEQRES 13 A 209 HIS ARG GLY GLU VAL LEU HIS VAL ASP ASP VAL PRO GLY SEQRES 14 A 209 ASP PRO ALA LEU VAL ALA THR VAL HIS PRO SER SER LEU SEQRES 15 A 209 LEU ARG GLY PRO LYS GLU GLU ARG GLU SER ALA PHE ALA SEQRES 16 A 209 GLY LEU VAL ASP ASP LEU ARG VAL ALA ALA ASP VAL ARG SEQRES 17 A 209 PRO HET SF4 A 301 8 HETNAM SF4 IRON/SULFUR CLUSTER FORMUL 2 SF4 FE4 S4 FORMUL 3 HOH *216(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 VAL A 174 N LEU A 138 SHEET 1 AA2 2 PHE A 98 THR A 99 0 SHEET 2 AA2 2 ILE A 108 SER A 109 -1 O ILE A 108 N THR A 99 LINK SG CYS A 24 FE3 SF4 A 301 1555 1555 2.36 LINK SG CYS A 27 FE2 SF4 A 301 1555 1555 2.40 LINK ND1 HIS A 95 FE4 SF4 A 301 1555 1555 2.10 LINK SG CYS A 120 FE1 SF4 A 301 1555 1555 2.30 SITE 1 AC1 6 CYS A 24 GLY A 26 CYS A 27 HIS A 95 SITE 2 AC1 6 CYS A 120 TRP A 123 CRYST1 36.229 51.393 54.444 90.00 105.21 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 0.027602 0.000000 0.007502 0.00000 SCALE2 0.000000 0.019458 0.000000 0.00000 SCALE3 0.000000 0.000000 0.019034 0.00000