HEADER HYDROLASE 15-MAR-22 7X9I TITLE CRYSTAL STRUCTURE OF MUTT-8-OXO-DGTP COMPLEX: REACTION FOR 12 HR USING TITLE 2 5 MM MN2+ COMPND MOL_ID: 1; COMPND 2 MOLECULE: 7,8-DIHYDRO-8-OXOGUANINE-TRIPHOSPHATASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: 8-OXO-DGTP DIPHOSPHATASE,8-OXO-DGTP DIPHOSPHATASE MUTT, COMPND 5 MUTATOR MUTT PROTEIN,MUTATOR MUTT PROTEIN (7,8-DIHYDRO-8-OXOGUANINE- COMPND 6 TRIPHOSPHATASE),NUCLEOSIDE TRIPHOSPHATE HYDROLASE,NUCLEOSIDE COMPND 7 TRIPHOSPHATE PYROPHOSPHOHYDROLASE,MARKED PREFERENCE FOR DGTP,DGTP- COMPND 8 PREFERRING NUCLEOSIDE TRIPHOSPHATE PYROPHOSPHOHYDROLASE; COMPND 9 EC: 3.6.1.55,3.6.1.-; COMPND 10 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS NUDIX HYDROLASE, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR T.NAKAMURA,Y.YAMAGATA REVDAT 2 29-NOV-23 7X9I 1 REMARK REVDAT 1 01-JUN-22 7X9I 0 JRNL AUTH T.NAKAMURA,Y.YAMAGATA JRNL TITL VISUALIZATION OF MUTAGENIC NUCLEOTIDE PROCESSING BY JRNL TITL 2 ESCHERICHIA COLI MUTT, A NUDIX HYDROLASE. JRNL REF PROC.NATL.ACAD.SCI.USA V. 119 18119 2022 JRNL REFN ESSN 1091-6490 JRNL PMID 35594391 JRNL DOI 10.1073/PNAS.2203118119 REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.13_2998 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 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 32.14 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 3 NUMBER OF REFLECTIONS : 10380 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.147 REMARK 3 R VALUE (WORKING SET) : 0.144 REMARK 3 FREE R VALUE : 0.190 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.210 REMARK 3 FREE R VALUE TEST SET COUNT : 541 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 32.1400 - 3.0200 1.00 2574 156 0.1480 0.1742 REMARK 3 2 3.0200 - 2.4000 1.00 2449 138 0.1493 0.2074 REMARK 3 3 2.4000 - 2.1000 0.99 2443 123 0.1381 0.1797 REMARK 3 4 2.1000 - 1.9000 0.98 2373 124 0.1348 0.2188 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) : 0.143 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 17.621 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 11.14 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 14.05 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 1204 REMARK 3 ANGLE : 1.342 1652 REMARK 3 CHIRALITY : 0.063 169 REMARK 3 PLANARITY : 0.005 203 REMARK 3 DIHEDRAL : 17.234 461 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 7X9I COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 20-MAR-22. REMARK 100 THE DEPOSITION ID IS D_1300028372. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 25-MAY-05 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL38B1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RIGAKU JUPITER 210 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 10412 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 32.140 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 200 DATA REDUNDANCY : 7.100 REMARK 200 R MERGE (I) : 0.05600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 32.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.97 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.16000 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: FOURIER SYNTHESIS REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: 3A6T REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.14 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.13 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: POTASSIUM SODIUM TARTRATE, SODIUM REMARK 280 CITRATE, AMMONIUM SULFATE, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 288K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-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 19.11950 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 29.67000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 28.00200 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 29.67000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 19.11950 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 28.00200 REMARK 290 SMTRY3 4 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 APPLY THE FOLLOWING TO CHAINS: A, C 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 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 447 DISTANCE = 6.21 ANGSTROMS 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 MN A 204 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLY A 37 O REMARK 620 2 GLU A 57 OE2 86.6 REMARK 620 3 8DG A 202 O2B 105.2 94.0 REMARK 620 4 8DG A 202 O1A 89.9 172.1 80.0 REMARK 620 5 8OG A 203 OP2 97.7 174.3 81.3 8.5 REMARK 620 6 HOH A 339 O 85.7 85.4 169.0 101.4 98.6 REMARK 620 7 HOH A 402 O 165.4 83.2 86.0 101.4 93.1 83.1 REMARK 620 8 HOH A 408 O 97.0 88.6 9.6 84.8 87.2 173.2 93.1 REMARK 620 N 1 2 3 4 5 6 7 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN A 205 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 53 OE2 REMARK 620 2 8DG A 202 O1B 96.2 REMARK 620 3 HOH A 301 O 75.6 107.2 REMARK 620 4 HOH A 302 O 160.6 96.8 86.8 REMARK 620 5 HOH A 323 O 91.7 161.4 91.1 80.4 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN A 206 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 53 OE1 REMARK 620 2 GLU A 57 OE2 92.1 REMARK 620 3 8DG A 202 O2B 107.0 75.6 REMARK 620 4 HOH A 307 O 152.1 62.9 79.7 REMARK 620 5 HOH A 311 O 106.2 106.3 146.7 72.4 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 207 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 53 OE1 REMARK 620 2 GLU A 57 OE2 90.6 REMARK 620 3 HOH A 307 O 145.4 58.5 REMARK 620 4 HOH A 311 O 106.2 98.9 67.6 REMARK 620 5 HOH A 355 O 88.1 158.3 126.4 102.2 REMARK 620 N 1 2 3 4 DBREF1 7X9I A 1 129 UNP A0A037YRW7_ECOLX DBREF2 7X9I A A0A037YRW7 1 129 SEQRES 1 A 129 MET LYS LYS LEU GLN ILE ALA VAL GLY ILE ILE ARG ASN SEQRES 2 A 129 GLU ASN ASN GLU ILE PHE ILE THR ARG ARG ALA ALA ASP SEQRES 3 A 129 ALA HIS MET ALA ASN LYS LEU GLU PHE PRO GLY GLY LYS SEQRES 4 A 129 ILE GLU MET GLY GLU THR PRO GLU GLN ALA VAL VAL ARG SEQRES 5 A 129 GLU LEU GLN GLU GLU VAL GLY ILE THR PRO GLN HIS PHE SEQRES 6 A 129 SER LEU PHE GLU LYS LEU GLU TYR GLU PHE PRO ASP ARG SEQRES 7 A 129 HIS ILE THR LEU TRP PHE TRP LEU VAL GLU ARG TRP GLU SEQRES 8 A 129 GLY GLU PRO TRP GLY LYS GLU GLY GLN PRO GLY GLU TRP SEQRES 9 A 129 MET SER LEU VAL GLY LEU ASN ALA ASP ASP PHE PRO PRO SEQRES 10 A 129 ALA ASN GLU PRO VAL ILE ALA LYS LEU LYS ARG LEU HET GLC C 1 11 HET FRU C 2 12 HET SO4 A 201 5 HET 8DG A 202 32 HET 8OG A 203 24 HET MN A 204 1 HET MN A 205 1 HET MN A 206 1 HET NA A 207 1 HETNAM GLC ALPHA-D-GLUCOPYRANOSE HETNAM FRU BETA-D-FRUCTOFURANOSE HETNAM SO4 SULFATE ION HETNAM 8DG 8-OXO-2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE HETNAM 8OG 8-OXO-2'-DEOXY-GUANOSINE-5'-MONOPHOSPHATE HETNAM MN MANGANESE (II) ION HETNAM NA SODIUM ION HETSYN GLC ALPHA-D-GLUCOSE; D-GLUCOSE; GLUCOSE HETSYN FRU BETA-D-FRUCTOSE; D-FRUCTOSE; FRUCTOSE HETSYN 8OG 8-OXO-7,8-DIHYDRO-2'-DEOXY-GUANOSINE-5'-MONOPHOSPHATE FORMUL 2 GLC C6 H12 O6 FORMUL 2 FRU C6 H12 O6 FORMUL 3 SO4 O4 S 2- FORMUL 4 8DG C10 H16 N5 O14 P3 FORMUL 5 8OG C10 H14 N5 O8 P FORMUL 6 MN 3(MN 2+) FORMUL 9 NA NA 1+ FORMUL 10 HOH *147(H2 O) HELIX 1 AA1 THR A 45 GLY A 59 1 15 HELIX 2 AA2 ASN A 111 PHE A 115 5 5 HELIX 3 AA3 PRO A 116 ALA A 118 5 3 HELIX 4 AA4 ASN A 119 ARG A 128 1 10 SHEET 1 AA1 4 GLY A 37 LYS A 39 0 SHEET 2 AA1 4 LYS A 2 ILE A 11 -1 N ALA A 7 O GLY A 38 SHEET 3 AA1 4 ARG A 78 VAL A 87 1 O TRP A 85 N ILE A 10 SHEET 4 AA1 4 SER A 66 GLU A 74 -1 N GLU A 69 O PHE A 84 SHEET 1 AA2 3 LEU A 33 GLU A 34 0 SHEET 2 AA2 3 GLU A 17 ARG A 22 -1 N THR A 21 O GLU A 34 SHEET 3 AA2 3 GLY A 102 SER A 106 -1 O MET A 105 N ILE A 18 SHEET 1 AA3 2 THR A 61 GLN A 63 0 SHEET 2 AA3 2 ARG A 89 GLU A 91 -1 O GLU A 91 N THR A 61 LINK C1 GLC C 1 O2 FRU C 2 1555 1555 1.41 LINK O GLY A 37 MN MN A 204 1555 1555 2.17 LINK OE2 GLU A 53 MN A MN A 205 1555 1555 2.67 LINK OE1 GLU A 53 MN A MN A 206 1555 1555 2.57 LINK OE1 GLU A 53 NA B NA A 207 1555 1555 2.46 LINK OE2 GLU A 57 MN MN A 204 1555 1555 2.31 LINK OE2 GLU A 57 MN A MN A 206 1555 1555 2.71 LINK OE2 GLU A 57 NA B NA A 207 1555 1555 2.87 LINK O2BA8DG A 202 MN MN A 204 1555 1555 2.12 LINK O1AA8DG A 202 MN MN A 204 1555 1555 2.22 LINK O1BA8DG A 202 MN A MN A 205 1555 1555 2.05 LINK O2BA8DG A 202 MN A MN A 206 1555 1555 2.58 LINK OP2B8OG A 203 MN MN A 204 1555 1555 2.27 LINK MN MN A 204 O HOH A 339 1555 1555 2.22 LINK MN MN A 204 O HOH A 402 1555 1555 2.32 LINK MN MN A 204 O CHOH A 408 1555 1555 2.17 LINK MN A MN A 205 O HOH A 301 1555 1555 2.53 LINK MN A MN A 205 O AHOH A 302 1555 1555 2.56 LINK MN A MN A 205 O HOH A 323 1555 1555 2.44 LINK MN A MN A 206 O HOH A 307 1555 1555 2.76 LINK MN A MN A 206 O HOH A 311 1555 1555 2.51 LINK NA B NA A 207 O HOH A 307 1555 1555 2.96 LINK NA B NA A 207 O HOH A 311 1555 1555 2.62 LINK NA B NA A 207 O BHOH A 355 1555 1555 3.04 CRYST1 38.239 56.004 59.340 90.00 90.00 90.00 P 21 21 21 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 0.026151 0.000000 0.000000 0.00000 SCALE2 0.000000 0.017856 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016852 0.00000