HEADER HYDROLASE 29-OCT-18 6IOC TITLE THE STRUCTURE OF THE H109Q MUTANT OF UDGX IN COMPLEX WITH URACIL COMPND MOL_ID: 1; COMPND 2 MOLECULE: PHAGE SPO1 DNA POLYMERASE-RELATED PROTEIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 7-215; COMPND 5 EC: 2.7.7.7; COMPND 6 ENGINEERED: YES; COMPND 7 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: MSMEI_0259; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS URACIL DNA GLYCOSYLASE, DNA REPAIR, IRON-SULFUR, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR W.XIE,J.TU REVDAT 2 22-NOV-23 6IOC 1 REMARK REVDAT 1 24-JUL-19 6IOC 0 JRNL AUTH J.TU,R.CHEN,Y.YANG,W.CAO,W.XIE JRNL TITL SUICIDE INACTIVATION OF THE URACIL DNA GLYCOSYLASE UDGX BY JRNL TITL 2 COVALENT COMPLEX FORMATION. JRNL REF NAT.CHEM.BIOL. V. 15 615 2019 JRNL REFN ESSN 1552-4469 JRNL PMID 31101915 JRNL DOI 10.1038/S41589-019-0290-X REMARK 2 REMARK 2 RESOLUTION. 1.62 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.10.1_2155: ???) 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) : 1.62 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.83 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.6 REMARK 3 NUMBER OF REFLECTIONS : 18216 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.156 REMARK 3 R VALUE (WORKING SET) : 0.155 REMARK 3 FREE R VALUE : 0.182 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.600 REMARK 3 FREE R VALUE TEST SET COUNT : 838 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 30.8323 - 2.9494 0.99 3052 155 0.1444 0.1430 REMARK 3 2 2.9494 - 2.3413 0.99 3025 144 0.1617 0.1949 REMARK 3 3 2.3413 - 2.0454 1.00 3005 157 0.1515 0.1970 REMARK 3 4 2.0454 - 1.8584 0.98 2946 167 0.1546 0.1979 REMARK 3 5 1.8584 - 1.7252 0.95 2899 114 0.1643 0.2165 REMARK 3 6 1.7252 - 1.6235 0.82 2451 101 0.1884 0.2481 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) : 0.160 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 19.350 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 : 0.012 1615 REMARK 3 ANGLE : 2.014 2196 REMARK 3 CHIRALITY : 0.063 246 REMARK 3 PLANARITY : 0.007 294 REMARK 3 DIHEDRAL : 17.647 960 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 6IOC COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 08-NOV-18. REMARK 100 THE DEPOSITION ID IS D_1300009442. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 23-SEP-18 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NFPSS REMARK 200 BEAMLINE : BL19U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.979 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 S 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : HKL-3000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 18944 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.620 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 3.800 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 200 DATA REDUNDANCY : 6.000 REMARK 200 R MERGE (I) : 0.12000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 14.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.62 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.65 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 4.70 REMARK 200 R MERGE FOR SHELL (I) : 0.57000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.800 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: 6IOA REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 27.41 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.69 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2.15M SODIUM MALONATE PH 7.0 AND 3.8% REMARK 280 MPD, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 298K 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 25.35550 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: 360 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 10120 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 LYS A 105 CG CD CE NZ REMARK 470 LYS A 110 CG CD CE NZ REMARK 470 ARG A 184 CG CD NE CZ NH1 NH2 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 NH2 ARG A 31 O HOH A 401 2.12 REMARK 500 O HOH A 448 O HOH A 470 2.13 REMARK 500 O HOH A 405 O HOH A 457 2.13 REMARK 500 O ARG A 184 O HOH A 402 2.16 REMARK 500 O HOH A 496 O HOH A 534 2.18 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 524 O HOH A 545 2546 2.14 REMARK 500 O HOH A 436 O HOH A 446 1655 2.15 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 FE2 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 24 SG REMARK 620 2 SF4 A 301 S1 119.9 REMARK 620 3 SF4 A 301 S3 117.6 101.9 REMARK 620 4 SF4 A 301 S4 105.7 105.3 105.1 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 CYS A 27 SG REMARK 620 2 SF4 A 301 S1 120.1 REMARK 620 3 SF4 A 301 S2 103.9 103.0 REMARK 620 4 SF4 A 301 S3 120.5 102.7 104.2 REMARK 620 N 1 2 3 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 HIS A 95 ND1 REMARK 620 2 SF4 A 301 S1 114.4 REMARK 620 3 SF4 A 301 S2 120.0 107.0 REMARK 620 4 SF4 A 301 S4 105.4 107.0 101.6 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 114.8 REMARK 620 3 SF4 A 301 S3 114.9 104.0 REMARK 620 4 SF4 A 301 S4 114.9 101.5 105.1 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 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue URA A 302 DBREF 6IOC A 1 209 UNP I7F541 I7F541_MYCS2 7 215 SEQADV 6IOC GLY A -2 UNP I7F541 EXPRESSION TAG SEQADV 6IOC SER A -1 UNP I7F541 EXPRESSION TAG SEQADV 6IOC HIS A 0 UNP I7F541 EXPRESSION TAG SEQADV 6IOC GLN A 109 UNP I7F541 HIS 115 ENGINEERED MUTATION SEQRES 1 A 212 GLY SER HIS MET ALA GLY ALA GLN ASP PHE VAL PRO HIS SEQRES 2 A 212 THR ALA ASP LEU ALA GLU LEU ALA ALA ALA ALA GLY GLU SEQRES 3 A 212 CYS ARG GLY CYS GLY LEU TYR ARG ASP ALA THR GLN ALA SEQRES 4 A 212 VAL PHE GLY ALA GLY GLY ARG SER ALA ARG ILE MET MET SEQRES 5 A 212 ILE GLY GLU GLN PRO GLY ASP LYS GLU ASP LEU ALA GLY SEQRES 6 A 212 LEU PRO PHE VAL GLY PRO ALA GLY ARG LEU LEU ASP ARG SEQRES 7 A 212 ALA LEU GLU ALA ALA ASP ILE ASP ARG ASP ALA LEU TYR SEQRES 8 A 212 VAL THR ASN ALA VAL LYS HIS PHE LYS PHE THR ARG ALA SEQRES 9 A 212 ALA GLY GLY LYS ARG ARG ILE GLN LYS THR PRO SER ARG SEQRES 10 A 212 THR GLU VAL VAL ALA CYS ARG PRO TRP LEU ILE ALA GLU SEQRES 11 A 212 MET THR SER VAL GLU PRO ASP VAL VAL VAL LEU LEU GLY SEQRES 12 A 212 ALA THR ALA ALA LYS ALA LEU LEU GLY ASN ASP PHE ARG SEQRES 13 A 212 VAL THR GLN HIS ARG GLY GLU VAL LEU HIS VAL ASP ASP SEQRES 14 A 212 VAL PRO GLY ASP PRO ALA LEU VAL ALA THR VAL HIS PRO SEQRES 15 A 212 SER SER LEU LEU ARG GLY PRO LYS GLU GLU ARG GLU SER SEQRES 16 A 212 ALA PHE ALA GLY LEU VAL ASP ASP LEU ARG VAL ALA ALA SEQRES 17 A 212 ASP VAL ARG PRO 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 *146(H2 O) HELIX 1 AA1 ALA A 2 VAL A 8 5 7 HELIX 2 AA2 ASP A 13 GLU A 23 1 11 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 ARG A 158 1 6 HELIX 10 AB1 HIS A 178 LEU A 183 5 6 HELIX 11 AB2 PRO A 186 VAL A 207 1 22 SHEET 1 AA1 5 LEU A 87 ASN A 91 0 SHEET 2 AA1 5 ILE A 47 GLY A 51 1 N MET A 49 O TYR A 88 SHEET 3 AA1 5 VAL A 135 LEU A 139 1 O VAL A 137 N MET A 48 SHEET 4 AA1 5 ALA A 172 THR A 176 1 O VAL A 174 N LEU A 138 SHEET 5 AA1 5 VAL A 161 LEU A 162 -1 N LEU A 162 O LEU A 173 LINK SG CYS A 24 FE2 SF4 A 301 1555 1555 2.34 LINK SG CYS A 27 FE4 SF4 A 301 1555 1555 2.33 LINK ND1 HIS A 95 FE3 SF4 A 301 1555 1555 2.04 LINK SG CYS A 120 FE1 SF4 A 301 1555 1555 2.24 CISPEP 1 ALA A 102 GLY A 103 0 -11.35 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 SITE 1 AC2 8 GLU A 52 GLN A 53 GLU A 58 PRO A 64 SITE 2 AC2 8 PHE A 65 ASN A 91 GLN A 109 HIS A 178 CRYST1 38.683 50.711 38.826 90.00 90.62 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 0.025851 0.000000 0.000281 0.00000 SCALE2 0.000000 0.019720 0.000000 0.00000 SCALE3 0.000000 0.000000 0.025757 0.00000