HEADER HYDROLASE 17-MAR-25 9MBF TITLE NEUTRON CRYSTAL STRUCTURE OF HUMAN MTH1(G2K/C87A/C104S MUTANT) IN TITLE 2 COMPLEX WITH 2-OXO-DATP COMPND MOL_ID: 1; COMPND 2 MOLECULE: 7,8-DIHYDRO-8-OXOGUANINE TRIPHOSPHATASE; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: 2-HYDROXY-DATP DIPHOSPHATASE,8-OXO-DGTPASE,NUCLEOSIDE COMPND 5 DIPHOSPHATE-LINKED MOIETY X MOTIF 1,NUDIX MOTIF 1; COMPND 6 EC: 3.6.1.55,3.6.1.56; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: NUDT1, MTH1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS OXIDIZED PURINE NUCLEOSIDE TRIPHOSPHATE HYDROLASE, HYDROLASE EXPDTA X-RAY DIFFRACTION; NEUTRON DIFFRACTION AUTHOR K.FUJIMIYA,Y.HIRANO,K.KUSAKA,T.TAMADA,T.NAKAMURA REVDAT 1 30-JUL-25 9MBF 0 JRNL AUTH K.HIRATA,K.FUJIMIYA,A.OSTERMANN,T.E.SCHRADER,T.HIROMOTO, JRNL AUTH 2 M.GOTO,T.ARIMORI,Y.HIRANO,K.KUSAKA,T.TAMADA,T.NAKAMURA JRNL TITL NEUTRON AND TIME-RESOLVED X-RAY CRYSTALLOGRAPHY REVEAL THE JRNL TITL 2 SUBSTRATE RECOGNITION AND CATALYTIC MECHANISM OF HUMAN NUDIX JRNL TITL 3 HYDROLASE MTH1. JRNL REF PROC.NATL.ACAD.SCI.USA V. 122 85122 2025 JRNL REFN ESSN 1091-6490 JRNL PMID 40674425 JRNL DOI 10.1073/PNAS.2510085122 REMARK 2 REMARK 2 RESOLUTION. 1.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 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 X-RAY DATA. REMARK 3 REMARK 3 REFINEMENT TARGET : GEOSTD + MONOMER LIBRARY REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 37.65 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.400 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 44602 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.176 REMARK 3 R VALUE (WORKING SET) : 0.175 REMARK 3 FREE R VALUE : 0.207 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.010 REMARK 3 FREE R VALUE TEST SET COUNT : 2235 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 37.6500 - 3.7800 1.00 2848 148 0.1696 0.1894 REMARK 3 2 3.7800 - 3.0000 1.00 2701 143 0.1553 0.1858 REMARK 3 3 3.0000 - 2.6200 1.00 2694 142 0.1721 0.1860 REMARK 3 4 2.6200 - 2.3800 1.00 2657 137 0.1757 0.2038 REMARK 3 5 2.3800 - 2.2100 1.00 2646 144 0.1689 0.2258 REMARK 3 6 2.2100 - 2.0800 1.00 2658 146 0.1687 0.1953 REMARK 3 7 2.0800 - 1.9800 1.00 2626 134 0.1729 0.2200 REMARK 3 8 1.9800 - 1.8900 1.00 2635 137 0.1822 0.2316 REMARK 3 9 1.8900 - 1.8200 1.00 2630 144 0.1842 0.2342 REMARK 3 10 1.8200 - 1.7500 1.00 2609 134 0.1892 0.2544 REMARK 3 11 1.7500 - 1.7000 1.00 2608 140 0.1920 0.2108 REMARK 3 12 1.7000 - 1.6500 1.00 2618 131 0.1952 0.2013 REMARK 3 13 1.6500 - 1.6100 1.00 2633 146 0.1851 0.2354 REMARK 3 14 1.6100 - 1.5700 1.00 2622 145 0.1892 0.2104 REMARK 3 15 1.5700 - 1.5300 1.00 2584 127 0.1981 0.2166 REMARK 3 16 1.5300 - 1.5000 1.00 2598 137 0.2022 0.2372 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) : 0.140 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 19.411 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 10.07 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 18.89 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 : 0.008 5808 REMARK 3 ANGLE : 1.037 10326 REMARK 3 CHIRALITY : 0.060 384 REMARK 3 PLANARITY : 0.006 1060 REMARK 3 DIHEDRAL : 20.909 1639 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 3 NEUTRON DATA. REMARK 3 REMARK 3 REFINEMENT TARGET : GEOSTD + MONOMER LIBRARY REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.75 REMARK 3 MIN(FOBS/SIGMA_FOBS) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 98.5 REMARK 3 NUMBER OF REFLECTIONS : 16235 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : NULL REMARK 3 R VALUE (WORKING SET) : NULL REMARK 3 FREE R VALUE : 0.246 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : NULL 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 2.2314 - 2.1000 0.00 2523 0 0.2118 0.2425 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) : 0.140 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 19.411 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 : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL 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 9MBF COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 17-MAR-25. REMARK 100 THE DEPOSITION ID IS D_1300052386. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-JUN-19 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 : PHOTON FACTORY REMARK 200 BEAMLINE : BL-5A 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 : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 44748 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.500 REMARK 200 RESOLUTION RANGE LOW (A) : 37.660 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 6.500 REMARK 200 R MERGE (I) : 0.03500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 36.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.59 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.07500 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: PHENIX REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 230 REMARK 230 EXPERIMENTAL DETAILS REMARK 230 EXPERIMENT TYPE : NEUTRON DIFFRACTION REMARK 230 DATE OF DATA COLLECTION : 06-MAR-19 REMARK 230 TEMPERATURE (KELVIN) : 100.0 REMARK 230 PH : NULL REMARK 230 NUMBER OF CRYSTALS USED : NULL REMARK 230 REMARK 230 NEUTRON SOURCE : SPALLATION SOURCE REMARK 230 BEAMLINE : BL-03 REMARK 230 WAVELENGTH OR RANGE (A) : 2.93-5.37 REMARK 230 MONOCHROMATOR : NULL REMARK 230 OPTICS : NULL REMARK 230 REMARK 230 DETECTOR TYPE : DIFFRACTOMETER REMARK 230 DETECTOR MANUFACTURER : IBIX REMARK 230 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 230 DATA SCALING SOFTWARE : XDS REMARK 230 REMARK 230 NUMBER OF UNIQUE REFLECTIONS : 16382 REMARK 230 RESOLUTION RANGE HIGH (A) : 2.100 REMARK 230 RESOLUTION RANGE LOW (A) : 19.750 REMARK 230 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 230 REMARK 230 OVERALL. REMARK 230 COMPLETENESS FOR RANGE (%) : 98.5 REMARK 230 DATA REDUNDANCY : 5.400 REMARK 230 R MERGE (I) : 0.22000 REMARK 230 R SYM (I) : NULL REMARK 230 FOR THE DATA SET : 7.8000 REMARK 230 REMARK 230 IN THE HIGHEST RESOLUTION SHELL. REMARK 230 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.10 REMARK 230 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.21 REMARK 230 COMPLETENESS FOR SHELL (%) : NULL REMARK 230 DATA REDUNDANCY IN SHELL : NULL REMARK 230 R MERGE FOR SHELL (I) : 0.53300 REMARK 230 R SYM FOR SHELL (I) : NULL REMARK 230 FOR SHELL : NULL REMARK 230 REMARK 230 METHOD USED TO DETERMINE THE STRUCTURE: FOURIER SYNTHESIS REMARK 230 SOFTWARE USED : PHENIX REMARK 230 STARTING MODEL: NULL REMARK 230 REMARK 230 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 35.02 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.89 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: SODIUM CITRATE, CACODYLATE, NACL, REMARK 280 VAPOR DIFFUSION, TEMPERATURE 293K 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 23.19300 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 61.94700 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 23.71050 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 61.94700 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 23.19300 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 23.71050 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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: 0 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 8420 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 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 350 REMARK 350 BIOMOLECULE: 2 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: 120 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 8080 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -11.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 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 ARG B 25 REMARK 465 GLY B 26 REMARK 465 PHE B 27 REMARK 465 GLY B 28 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 ASP A 89 -92.44 -90.51 REMARK 500 GLN A 110 36.40 -140.94 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 NA A 203 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 52 OE2 REMARK 620 2 6U4 A 201 O2B 98.8 REMARK 620 3 HOH A 311 O 81.4 81.4 REMARK 620 4 HOH A 331 O 168.3 92.8 99.3 REMARK 620 5 HOH A 337 O 92.3 167.0 93.7 76.0 REMARK 620 6 HOH A 367 O 82.1 98.3 163.2 97.5 89.9 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 202 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 6U4 A 201 O1B REMARK 620 2 6U4 A 201 O1A 86.2 REMARK 620 3 HOH A 306 O 52.1 126.1 REMARK 620 4 HOH A 341 O 93.2 85.3 124.0 REMARK 620 5 HOH A 370 O 84.7 95.9 53.6 177.5 REMARK 620 6 HOH A 389 O 82.9 168.8 46.9 93.0 85.3 REMARK 620 7 HOH A 450 O 167.9 103.1 115.9 95.2 86.6 88.1 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA B 203 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLY B 36 O REMARK 620 2 GLU B 56 OE2 82.6 REMARK 620 3 6U4 B 201 O1B 116.3 104.2 REMARK 620 4 6U4 B 201 O1A 115.5 160.8 74.4 REMARK 620 5 HOH B 361 O 78.9 75.6 164.8 100.7 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA B 202 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU B 52 OE2 REMARK 620 2 6U4 B 201 O2B 109.5 REMARK 620 3 HOH B 342 O 73.2 89.8 REMARK 620 N 1 2 DBREF 9MBF A 1 156 UNP P36639 8ODP_HUMAN 42 197 DBREF 9MBF B 1 156 UNP P36639 8ODP_HUMAN 42 197 SEQADV 9MBF LYS A 2 UNP P36639 GLY 43 ENGINEERED MUTATION SEQADV 9MBF ALA A 87 UNP P36639 CYS 128 ENGINEERED MUTATION SEQADV 9MBF SER A 104 UNP P36639 CYS 145 ENGINEERED MUTATION SEQADV 9MBF LYS B 2 UNP P36639 GLY 43 ENGINEERED MUTATION SEQADV 9MBF ALA B 87 UNP P36639 CYS 128 ENGINEERED MUTATION SEQADV 9MBF SER B 104 UNP P36639 CYS 145 ENGINEERED MUTATION SEQRES 1 A 156 MET LYS ALA SER ARG LEU TYR THR LEU VAL LEU VAL LEU SEQRES 2 A 156 GLN PRO GLN ARG VAL LEU LEU GLY MET LYS LYS ARG GLY SEQRES 3 A 156 PHE GLY ALA GLY ARG TRP ASN GLY PHE GLY GLY LYS VAL SEQRES 4 A 156 GLN GLU GLY GLU THR ILE GLU ASP GLY ALA ARG ARG GLU SEQRES 5 A 156 LEU GLN GLU GLU SER GLY LEU THR VAL ASP ALA LEU HIS SEQRES 6 A 156 LYS VAL GLY GLN ILE VAL PHE GLU PHE VAL GLY GLU PRO SEQRES 7 A 156 GLU LEU MET ASP VAL HIS VAL PHE ALA THR ASP SER ILE SEQRES 8 A 156 GLN GLY THR PRO VAL GLU SER ASP GLU MET ARG PRO SER SEQRES 9 A 156 TRP PHE GLN LEU ASP GLN ILE PRO PHE LYS ASP MET TRP SEQRES 10 A 156 PRO ASP ASP SER TYR TRP PHE PRO LEU LEU LEU GLN LYS SEQRES 11 A 156 LYS LYS PHE HIS GLY TYR PHE LYS PHE GLN GLY GLN ASP SEQRES 12 A 156 THR ILE LEU ASP TYR THR LEU ARG GLU VAL ASP THR VAL SEQRES 1 B 156 MET LYS ALA SER ARG LEU TYR THR LEU VAL LEU VAL LEU SEQRES 2 B 156 GLN PRO GLN ARG VAL LEU LEU GLY MET LYS LYS ARG GLY SEQRES 3 B 156 PHE GLY ALA GLY ARG TRP ASN GLY PHE GLY GLY LYS VAL SEQRES 4 B 156 GLN GLU GLY GLU THR ILE GLU ASP GLY ALA ARG ARG GLU SEQRES 5 B 156 LEU GLN GLU GLU SER GLY LEU THR VAL ASP ALA LEU HIS SEQRES 6 B 156 LYS VAL GLY GLN ILE VAL PHE GLU PHE VAL GLY GLU PRO SEQRES 7 B 156 GLU LEU MET ASP VAL HIS VAL PHE ALA THR ASP SER ILE SEQRES 8 B 156 GLN GLY THR PRO VAL GLU SER ASP GLU MET ARG PRO SER SEQRES 9 B 156 TRP PHE GLN LEU ASP GLN ILE PRO PHE LYS ASP MET TRP SEQRES 10 B 156 PRO ASP ASP SER TYR TRP PHE PRO LEU LEU LEU GLN LYS SEQRES 11 B 156 LYS LYS PHE HIS GLY TYR PHE LYS PHE GLN GLY GLN ASP SEQRES 12 B 156 THR ILE LEU ASP TYR THR LEU ARG GLU VAL ASP THR VAL HET 6U4 A 201 44 HET NA A 202 1 HET NA A 203 1 HET 6U4 B 201 43 HET NA B 202 1 HET NA B 203 1 HETNAM 6U4 [[(2R,3S,5R)-5-(6-AZANYL-2-OXIDANYLIDENE-1H-PURIN-9- HETNAM 2 6U4 YL)-3-OXIDANYL-OXOLAN-2-YL]METHOXY-OXIDANYL- HETNAM 3 6U4 PHOSPHORYL] PHOSPHONO HYDROGEN PHOSPHATE HETNAM NA SODIUM ION HETSYN 6U4 2-OXO-DATP FORMUL 3 6U4 2(C10 H16 N5 O13 P3) FORMUL 4 NA 4(NA 1+) FORMUL 9 HOH *288(H2 O) HELIX 1 AA1 THR A 44 GLY A 58 1 15 HELIX 2 AA2 PRO A 112 MET A 116 5 5 HELIX 3 AA3 TRP A 117 PRO A 118 5 2 HELIX 4 AA4 ASP A 119 GLN A 129 1 11 HELIX 5 AA5 THR B 44 GLY B 58 1 15 HELIX 6 AA6 PRO B 112 MET B 116 5 5 HELIX 7 AA7 TRP B 117 PRO B 118 5 2 HELIX 8 AA8 ASP B 119 GLN B 129 1 11 SHEET 1 AA1 3 TRP A 32 ASN A 33 0 SHEET 2 AA1 3 ARG A 17 LYS A 23 -1 N GLY A 21 O ASN A 33 SHEET 3 AA1 3 MET A 101 GLN A 107 -1 O ARG A 102 N MET A 22 SHEET 1 AA2 7 TRP A 32 ASN A 33 0 SHEET 2 AA2 7 ARG A 17 LYS A 23 -1 N GLY A 21 O ASN A 33 SHEET 3 AA2 7 SER A 4 LEU A 13 -1 N VAL A 12 O LEU A 19 SHEET 4 AA2 7 LEU A 80 THR A 88 1 O PHE A 86 N LEU A 9 SHEET 5 AA2 7 HIS A 65 PHE A 74 -1 N ILE A 70 O VAL A 83 SHEET 6 AA2 7 LYS A 132 GLN A 140 1 O PHE A 139 N GLU A 73 SHEET 7 AA2 7 THR A 144 VAL A 153 -1 O ASP A 147 N LYS A 138 SHEET 1 AA3 3 TRP B 32 ASN B 33 0 SHEET 2 AA3 3 ARG B 17 LYS B 23 -1 N GLY B 21 O ASN B 33 SHEET 3 AA3 3 MET B 101 GLN B 107 -1 O ARG B 102 N MET B 22 SHEET 1 AA4 7 TRP B 32 ASN B 33 0 SHEET 2 AA4 7 ARG B 17 LYS B 23 -1 N GLY B 21 O ASN B 33 SHEET 3 AA4 7 SER B 4 GLN B 14 -1 N GLN B 14 O ARG B 17 SHEET 4 AA4 7 LEU B 80 GLN B 92 1 O ASP B 82 N ARG B 5 SHEET 5 AA4 7 THR B 60 PHE B 74 -1 N VAL B 67 O VAL B 85 SHEET 6 AA4 7 PHE B 133 GLN B 140 1 O PHE B 139 N GLU B 73 SHEET 7 AA4 7 THR B 144 GLU B 152 -1 O ASP B 147 N LYS B 138 LINK OE2 GLU A 52 NA NA A 203 1555 1555 2.40 LINK O1B 6U4 A 201 NA NA A 202 1555 1555 2.30 LINK O1A 6U4 A 201 NA NA A 202 1555 1555 2.29 LINK O2B 6U4 A 201 NA NA A 203 1555 1555 2.39 LINK NA NA A 202 O AHOH A 306 1555 1555 3.20 LINK NA NA A 202 O HOH A 341 1555 1555 2.35 LINK NA NA A 202 O HOH A 370 1555 1555 2.50 LINK NA NA A 202 O HOH A 389 1555 1555 2.52 LINK NA NA A 202 O HOH A 450 1555 1555 2.33 LINK NA NA A 203 O HOH A 311 1555 1555 2.33 LINK NA NA A 203 O HOH A 331 1555 1555 2.36 LINK NA NA A 203 O HOH A 337 1555 1555 2.41 LINK NA NA A 203 O HOH A 367 1555 1555 2.37 LINK O GLY B 36 NA NA B 203 1555 1555 2.41 LINK OE2 GLU B 52 NA NA B 202 1555 1555 2.44 LINK OE2 GLU B 56 NA NA B 203 1555 1555 2.32 LINK O2B 6U4 B 201 NA NA B 202 1555 1555 2.58 LINK O1B 6U4 B 201 NA NA B 203 1555 1555 2.65 LINK O1A 6U4 B 201 NA NA B 203 1555 1555 2.25 LINK NA NA B 202 O HOH B 342 1555 1555 2.82 LINK NA NA B 203 O HOH B 361 1555 1555 2.25 CRYST1 46.386 47.421 123.894 90.00 90.00 90.00 P 21 21 21 8 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 0.021558 0.000000 0.000000 0.00000 SCALE2 0.000000 0.021088 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008071 0.00000 CONECT 905 5580 CONECT 3443 5625 CONECT 3701 5624 CONECT 3771 5625 CONECT 5535 5536 5537 5538 5542 CONECT 5536 5535 CONECT 5537 5535 CONECT 5538 5535 CONECT 5539 5540 5541 5542 5546 CONECT 5540 5539 5579 CONECT 5541 5539 5580 CONECT 5542 5535 5539 CONECT 5543 5544 5545 5546 5547 CONECT 5544 5543 CONECT 5545 5543 5579 CONECT 5546 5539 5543 CONECT 5547 5543 5548 CONECT 5548 5547 5549 5566 5567 CONECT 5549 5548 5550 5551 5568 CONECT 5550 5549 5554 CONECT 5551 5549 5552 5553 5569 CONECT 5552 5551 CONECT 5553 5551 5554 5571 5572 CONECT 5554 5550 5553 5555 5573 CONECT 5555 5554 5556 5564 CONECT 5556 5555 5557 5574 CONECT 5557 5556 5558 CONECT 5558 5557 5559 5564 CONECT 5559 5558 5560 5561 CONECT 5560 5559 5576 CONECT 5561 5559 5562 CONECT 5562 5561 5563 5565 CONECT 5563 5562 5564 CONECT 5564 5555 5558 5563 CONECT 5565 5562 CONECT 5566 5548 CONECT 5567 5548 CONECT 5568 5549 CONECT 5569 5551 CONECT 5571 5553 CONECT 5572 5553 CONECT 5573 5554 CONECT 5574 5556 CONECT 5576 5560 CONECT 5579 5540 5545 5633 5680 CONECT 5579 5729 5761 5841 CONECT 5580 905 5541 5639 5665 CONECT 5580 5674 5724 CONECT 5581 5582 5583 5584 5588 CONECT 5582 5581 CONECT 5583 5581 CONECT 5584 5581 CONECT 5585 5586 5587 5588 5592 CONECT 5586 5585 5625 CONECT 5587 5585 5624 CONECT 5588 5581 5585 CONECT 5589 5590 5591 5592 5593 CONECT 5590 5589 CONECT 5591 5589 5625 CONECT 5592 5585 5589 CONECT 5593 5589 5594 CONECT 5594 5593 5595 5612 5613 CONECT 5595 5594 5596 5597 5614 CONECT 5596 5595 5600 CONECT 5597 5595 5598 5599 5615 CONECT 5598 5597 CONECT 5599 5597 5600 5616 5617 CONECT 5600 5596 5599 5601 5618 CONECT 5601 5600 5602 5610 CONECT 5602 5601 5603 5619 CONECT 5603 5602 5604 CONECT 5604 5603 5605 5610 CONECT 5605 5604 5606 5607 CONECT 5606 5605 5620 CONECT 5607 5605 5608 CONECT 5608 5607 5609 5611 CONECT 5609 5608 5610 CONECT 5610 5601 5604 5609 CONECT 5611 5608 CONECT 5612 5594 CONECT 5613 5594 CONECT 5614 5595 CONECT 5615 5597 CONECT 5616 5599 CONECT 5617 5599 CONECT 5618 5600 CONECT 5619 5602 CONECT 5620 5606 CONECT 5624 3701 5587 5926 CONECT 5625 3443 3771 5586 5591 CONECT 5625 5958 CONECT 5633 5579 CONECT 5639 5580 CONECT 5665 5580 CONECT 5674 5580 CONECT 5680 5579 CONECT 5724 5580 CONECT 5729 5579 CONECT 5761 5579 CONECT 5841 5579 CONECT 5926 5624 CONECT 5958 5625 MASTER 403 0 6 8 20 0 0 6 2864 2 102 24 END