HEADER HYDROLASE 12-AUG-16 5LPG TITLE STRUCTURE OF NUDT15 IN COMPLEX WITH 6-THIO-GMP COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROBABLE 8-OXO-DGTP DIPHOSPHATASE NUDT15; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: 8-OXO-DGTPASE NUDT15,7,8-DIHYDRO-8-OXOGUANINE-TRIPHOSPHATASE COMPND 5 NUDT15,MUTT HOMOLOG 2,MTH2,NUCLEOSIDE DIPHOSPHATE-LINKED MOIETY X COMPND 6 MOTIF 15,NUDIX MOTIF 15; COMPND 7 EC: 3.6.1.55; COMPND 8 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: NUDT15, MTH2; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET28A(+) KEYWDS MTH2, DNA REPAIR ENZYME, CANCER, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR G.MASUYER,M.CARTER,D.REHLING,P.STENMARK,T.HELLEDAY,A.-S.JEMTH, AUTHOR 2 N.C.K.VALERIE,E.HOMAN,P.HERR,L.BEVC,B.D.G.PAGE,A.HAGENKORT REVDAT 4 10-JAN-24 5LPG 1 LINK REVDAT 3 28-SEP-16 5LPG 1 JRNL REVDAT 2 14-SEP-16 5LPG 1 JRNL REVDAT 1 24-AUG-16 5LPG 0 JRNL AUTH N.C.VALERIE,A.HAGENKORT,B.D.PAGE,G.MASUYER,D.REHLING, JRNL AUTH 2 M.CARTER,L.BEVC,P.HERR,E.HOMAN,N.G.SHEPPARD,P.STENMARK, JRNL AUTH 3 A.S.JEMTH,T.HELLEDAY JRNL TITL NUDT15 HYDROLYZES 6-THIO-DEOXYGTP TO MEDIATE THE ANTICANCER JRNL TITL 2 EFFICACY OF 6-THIOGUANINE. JRNL REF CANCER RES. V. 76 5501 2016 JRNL REFN ESSN 1538-7445 JRNL PMID 27530327 JRNL DOI 10.1158/0008-5472.CAN-16-0584 REMARK 2 REMARK 2 RESOLUTION. 1.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0135 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 49.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 33174 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : FREE R-VALUE REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.218 REMARK 3 R VALUE (WORKING SET) : 0.216 REMARK 3 FREE R VALUE : 0.251 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1751 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.70 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.74 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2437 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.88 REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE SET COUNT : 111 REMARK 3 BIN FREE R VALUE : 0.4390 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2489 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 29 REMARK 3 SOLVENT ATOMS : 156 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 39.14 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.16000 REMARK 3 B22 (A**2) : 1.28000 REMARK 3 B33 (A**2) : -1.44000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.130 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.124 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.126 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 8.326 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.962 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.950 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2612 ; 0.010 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 2376 ; 0.003 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3556 ; 1.419 ; 1.948 REMARK 3 BOND ANGLES OTHERS (DEGREES): 5494 ; 0.903 ; 3.003 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 314 ; 6.806 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 127 ;33.906 ;24.567 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 417 ;12.570 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 10 ;15.489 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 363 ; 0.084 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2974 ; 0.007 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 615 ; 0.002 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 1256 ; 2.561 ; 2.747 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1255 ; 2.561 ; 2.747 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1570 ; 4.002 ; 4.107 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 1571 ; 4.001 ; 4.108 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1356 ; 3.062 ; 3.172 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1356 ; 3.062 ; 3.172 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 1986 ; 4.946 ; 4.597 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 3091 ; 7.559 ;23.601 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 3013 ; 7.525 ;23.299 REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 2 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 9 A 1101 REMARK 3 ORIGIN FOR THE GROUP (A): -9.3946 -9.0353 18.8891 REMARK 3 T TENSOR REMARK 3 T11: 0.1186 T22: 0.0469 REMARK 3 T33: 0.0521 T12: -0.0200 REMARK 3 T13: 0.0194 T23: 0.0040 REMARK 3 L TENSOR REMARK 3 L11: 0.5442 L22: 0.6243 REMARK 3 L33: 0.7581 L12: 0.5414 REMARK 3 L13: 0.4752 L23: 0.6180 REMARK 3 S TENSOR REMARK 3 S11: -0.0529 S12: 0.0642 S13: -0.1067 REMARK 3 S21: -0.1356 S22: 0.1226 S23: -0.0794 REMARK 3 S31: -0.2484 S32: 0.1010 S33: -0.0697 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 9 B 1104 REMARK 3 ORIGIN FOR THE GROUP (A): -27.2104 -28.7267 13.9091 REMARK 3 T TENSOR REMARK 3 T11: 0.0885 T22: 0.1202 REMARK 3 T33: 0.0611 T12: -0.0172 REMARK 3 T13: 0.0236 T23: -0.0206 REMARK 3 L TENSOR REMARK 3 L11: 0.7181 L22: 0.7725 REMARK 3 L33: 2.7809 L12: 0.6171 REMARK 3 L13: 1.3820 L23: 1.3089 REMARK 3 S TENSOR REMARK 3 S11: 0.1777 S12: -0.2307 S13: -0.0266 REMARK 3 S21: 0.0130 S22: -0.1451 S23: -0.1291 REMARK 3 S31: 0.1726 S32: -0.4915 S33: -0.0326 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 5LPG COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 13-AUG-16. REMARK 100 THE DEPOSITION ID IS D_1200001159. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 31-OCT-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID29 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.072 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 : IMOSFLM REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 34988 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 REMARK 200 RESOLUTION RANGE LOW (A) : 49.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 11.80 REMARK 200 R MERGE (I) : 0.08700 REMARK 200 R SYM (I) : 0.03700 REMARK 200 FOR THE DATA SET : 12.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.73 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 11.50 REMARK 200 R MERGE FOR SHELL (I) : 0.68000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.400 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: PDB 5BON REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.10 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 30% PEG3350, 0.1M TRIS PH 8.5, AND REMARK 280 0.24M MGCL2, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 294K 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 23.25100 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 67.78000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 24.52500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 67.78000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 23.25100 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 24.52500 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3870 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 13420 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -64.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 MET A 1 REMARK 465 THR A 2 REMARK 465 ALA A 3 REMARK 465 SER A 4 REMARK 465 ALA A 5 REMARK 465 GLN A 6 REMARK 465 PRO A 7 REMARK 465 ARG A 8 REMARK 465 MET B 1 REMARK 465 THR B 2 REMARK 465 ALA B 3 REMARK 465 SER B 4 REMARK 465 ALA B 5 REMARK 465 GLN B 6 REMARK 465 PRO B 7 REMARK 465 ARG B 8 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 ARG A 10 CG CD NE CZ NH1 NH2 REMARK 470 ARG B 27 CG CD NE CZ NH1 NH2 REMARK 470 GLU B 127 CG CD OE1 OE2 REMARK 470 ASP B 132 CG OD1 OD2 REMARK 470 GLN B 133 CG CD OE1 NE2 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 NZ LYS B 142 O HOH B 1201 2.17 REMARK 500 REMARK 500 REMARK: NULL 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 GLU A 113 72.98 -117.92 REMARK 500 GLU B 113 73.76 -115.58 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 MG A1101 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 63 OE1 REMARK 620 2 GLU A 67 OE2 90.5 REMARK 620 3 HOH A1210 O 94.3 169.7 REMARK 620 4 HOH A1211 O 99.8 88.8 81.4 REMARK 620 5 HOH A1228 O 80.5 97.1 92.7 174.1 REMARK 620 6 HOH A1263 O 167.8 90.8 86.4 92.3 87.3 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B1104 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A1271 O REMARK 620 2 GLU B 63 OE2 176.2 REMARK 620 3 HOH B1214 O 94.7 88.3 REMARK 620 4 HOH B1220 O 86.3 91.0 95.5 REMARK 620 5 HOH B1243 O 87.7 94.7 91.2 171.4 REMARK 620 6 HOH B1267 O 84.4 92.4 176.2 80.7 92.5 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B1102 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLY B 47 O REMARK 620 2 GLU B 67 OE2 88.1 REMARK 620 3 HOH B1215 O 93.0 82.3 REMARK 620 4 HOH B1227 O 86.5 88.5 170.9 REMARK 620 5 HOH B1254 O 171.4 85.6 92.1 87.3 REMARK 620 6 HOH B1257 O 90.4 177.7 96.1 93.1 96.0 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B1101 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU B 63 OE1 REMARK 620 2 GLU B 67 OE2 81.9 REMARK 620 3 HOH B1209 O 164.2 84.4 REMARK 620 4 HOH B1215 O 91.7 76.2 92.7 REMARK 620 5 HOH B1230 O 88.6 101.4 86.3 177.5 REMARK 620 6 HOH B1267 O 101.6 171.0 93.1 95.3 87.0 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B1103 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH B1215 O REMARK 620 2 HOH B1243 O 114.8 REMARK 620 3 HOH B1264 O 123.8 109.2 REMARK 620 4 HOH B1283 O 110.9 93.1 99.5 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 MG A 1101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 71V A 1102 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG B 1101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG B 1102 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG B 1103 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG B 1104 DBREF 5LPG A 1 164 UNP Q9NV35 NUD15_HUMAN 1 164 DBREF 5LPG B 1 164 UNP Q9NV35 NUD15_HUMAN 1 164 SEQRES 1 A 164 MET THR ALA SER ALA GLN PRO ARG GLY ARG ARG PRO GLY SEQRES 2 A 164 VAL GLY VAL GLY VAL VAL VAL THR SER CYS LYS HIS PRO SEQRES 3 A 164 ARG CYS VAL LEU LEU GLY LYS ARG LYS GLY SER VAL GLY SEQRES 4 A 164 ALA GLY SER PHE GLN LEU PRO GLY GLY HIS LEU GLU PHE SEQRES 5 A 164 GLY GLU THR TRP GLU GLU CYS ALA GLN ARG GLU THR TRP SEQRES 6 A 164 GLU GLU ALA ALA LEU HIS LEU LYS ASN VAL HIS PHE ALA SEQRES 7 A 164 SER VAL VAL ASN SER PHE ILE GLU LYS GLU ASN TYR HIS SEQRES 8 A 164 TYR VAL THR ILE LEU MET LYS GLY GLU VAL ASP VAL THR SEQRES 9 A 164 HIS ASP SER GLU PRO LYS ASN VAL GLU PRO GLU LYS ASN SEQRES 10 A 164 GLU SER TRP GLU TRP VAL PRO TRP GLU GLU LEU PRO PRO SEQRES 11 A 164 LEU ASP GLN LEU PHE TRP GLY LEU ARG CYS LEU LYS GLU SEQRES 12 A 164 GLN GLY TYR ASP PRO PHE LYS GLU ASP LEU ASN HIS LEU SEQRES 13 A 164 VAL GLY TYR LYS GLY ASN HIS LEU SEQRES 1 B 164 MET THR ALA SER ALA GLN PRO ARG GLY ARG ARG PRO GLY SEQRES 2 B 164 VAL GLY VAL GLY VAL VAL VAL THR SER CYS LYS HIS PRO SEQRES 3 B 164 ARG CYS VAL LEU LEU GLY LYS ARG LYS GLY SER VAL GLY SEQRES 4 B 164 ALA GLY SER PHE GLN LEU PRO GLY GLY HIS LEU GLU PHE SEQRES 5 B 164 GLY GLU THR TRP GLU GLU CYS ALA GLN ARG GLU THR TRP SEQRES 6 B 164 GLU GLU ALA ALA LEU HIS LEU LYS ASN VAL HIS PHE ALA SEQRES 7 B 164 SER VAL VAL ASN SER PHE ILE GLU LYS GLU ASN TYR HIS SEQRES 8 B 164 TYR VAL THR ILE LEU MET LYS GLY GLU VAL ASP VAL THR SEQRES 9 B 164 HIS ASP SER GLU PRO LYS ASN VAL GLU PRO GLU LYS ASN SEQRES 10 B 164 GLU SER TRP GLU TRP VAL PRO TRP GLU GLU LEU PRO PRO SEQRES 11 B 164 LEU ASP GLN LEU PHE TRP GLY LEU ARG CYS LEU LYS GLU SEQRES 12 B 164 GLN GLY TYR ASP PRO PHE LYS GLU ASP LEU ASN HIS LEU SEQRES 13 B 164 VAL GLY TYR LYS GLY ASN HIS LEU HET MG A1101 1 HET 71V A1102 24 HET MG B1101 1 HET MG B1102 1 HET MG B1103 1 HET MG B1104 1 HETNAM MG MAGNESIUM ION HETNAM 71V [(2~{R},3~{S},4~{R},5~{R})-5-(2-AZANYL-6-SULFANYL- HETNAM 2 71V PURIN-9-YL)-3,4-BIS(OXIDANYL)OXOLAN-2-YL]METHYL HETNAM 3 71V DIHYDROGEN PHOSPHATE HETSYN 71V 6-THIO-GMP FORMUL 3 MG 5(MG 2+) FORMUL 4 71V C10 H14 N5 O7 P S FORMUL 9 HOH *156(H2 O) HELIX 1 AA1 THR A 55 ALA A 69 1 15 HELIX 2 AA2 GLU A 86 ASN A 89 5 4 HELIX 3 AA3 GLU A 126 LEU A 128 5 3 HELIX 4 AA4 PRO A 130 LEU A 134 5 5 HELIX 5 AA5 PHE A 135 GLN A 144 1 10 HELIX 6 AA6 LEU A 153 VAL A 157 5 5 HELIX 7 AA7 THR B 55 ALA B 69 1 15 HELIX 8 AA8 GLU B 86 ASN B 89 5 4 HELIX 9 AA9 PRO B 130 LEU B 134 5 5 HELIX 10 AB1 PHE B 135 GLN B 144 1 10 HELIX 11 AB2 LEU B 153 VAL B 157 5 5 SHEET 1 AA1 4 GLY A 47 HIS A 49 0 SHEET 2 AA1 4 GLY A 13 THR A 21 -1 N VAL A 16 O GLY A 48 SHEET 3 AA1 4 TYR A 90 VAL A 101 1 O MET A 97 N VAL A 19 SHEET 4 AA1 4 LEU A 72 ILE A 85 -1 N ILE A 85 O TYR A 90 SHEET 1 AA2 3 PHE A 43 GLN A 44 0 SHEET 2 AA2 3 CYS A 28 ARG A 34 -1 N GLY A 32 O GLN A 44 SHEET 3 AA2 3 ASN A 117 PRO A 124 -1 O GLU A 118 N LYS A 33 SHEET 1 AA3 4 GLY B 47 HIS B 49 0 SHEET 2 AA3 4 GLY B 13 THR B 21 -1 N VAL B 16 O GLY B 48 SHEET 3 AA3 4 TYR B 90 VAL B 101 1 O MET B 97 N VAL B 19 SHEET 4 AA3 4 LEU B 72 ILE B 85 -1 N SER B 79 O LEU B 96 SHEET 1 AA4 3 PHE B 43 GLN B 44 0 SHEET 2 AA4 3 CYS B 28 LYS B 33 -1 N GLY B 32 O GLN B 44 SHEET 3 AA4 3 GLU B 121 PRO B 124 -1 O VAL B 123 N VAL B 29 LINK OE1 GLU A 63 MG MG A1101 1555 1555 2.20 LINK OE2 GLU A 67 MG MG A1101 1555 1555 2.11 LINK MG MG A1101 O HOH A1210 1555 1555 2.02 LINK MG MG A1101 O HOH A1211 1555 1555 2.08 LINK MG MG A1101 O HOH A1228 1555 1555 2.09 LINK MG MG A1101 O HOH A1263 1555 1555 2.37 LINK O HOH A1271 MG MG B1104 1555 1555 2.30 LINK O GLY B 47 MG MG B1102 1555 1555 2.14 LINK OE1 GLU B 63 MG MG B1101 1555 1555 2.13 LINK OE2 GLU B 63 MG MG B1104 1555 1555 2.12 LINK OE2 GLU B 67 MG MG B1101 1555 1555 2.24 LINK OE2 GLU B 67 MG MG B1102 1555 1555 2.18 LINK MG MG B1101 O HOH B1209 1555 1555 2.09 LINK MG MG B1101 O HOH B1215 1555 1555 2.08 LINK MG MG B1101 O HOH B1230 1555 1555 2.05 LINK MG MG B1101 O HOH B1267 1555 1555 2.15 LINK MG MG B1102 O HOH B1215 1555 1555 1.86 LINK MG MG B1102 O HOH B1227 1555 1555 2.11 LINK MG MG B1102 O HOH B1254 1555 1555 2.16 LINK MG MG B1102 O HOH B1257 1555 1555 2.08 LINK MG MG B1103 O HOH B1215 1555 1555 1.70 LINK MG MG B1103 O HOH B1243 1555 1555 1.71 LINK MG MG B1103 O HOH B1264 1555 1555 1.89 LINK MG MG B1103 O HOH B1283 1555 1555 1.84 LINK MG MG B1104 O HOH B1214 1555 1555 1.94 LINK MG MG B1104 O HOH B1220 1555 1555 2.19 LINK MG MG B1104 O HOH B1243 1555 1555 1.99 LINK MG MG B1104 O HOH B1267 1555 1555 2.20 SITE 1 AC1 7 GLY A 47 GLU A 63 GLU A 67 HOH A1210 SITE 2 AC1 7 HOH A1211 HOH A1228 HOH A1263 SITE 1 AC2 13 ARG A 34 LEU A 45 PRO A 46 GLY A 47 SITE 2 AC2 13 GLY A 48 HIS A 49 TYR A 90 PHE A 135 SITE 3 AC2 13 GLY A 137 LEU A 138 HOH A1211 HOH A1218 SITE 4 AC2 13 HOH A1227 SITE 1 AC3 9 GLU B 63 GLU B 67 MG B1102 MG B1103 SITE 2 AC3 9 MG B1104 HOH B1209 HOH B1215 HOH B1230 SITE 3 AC3 9 HOH B1267 SITE 1 AC4 8 GLY B 47 GLU B 67 MG B1101 MG B1103 SITE 2 AC4 8 HOH B1215 HOH B1227 HOH B1254 HOH B1257 SITE 1 AC5 8 GLY B 48 MG B1101 MG B1102 MG B1104 SITE 2 AC5 8 HOH B1215 HOH B1243 HOH B1264 HOH B1283 SITE 1 AC6 8 HOH A1271 GLU B 63 MG B1101 MG B1103 SITE 2 AC6 8 HOH B1214 HOH B1220 HOH B1243 HOH B1267 CRYST1 46.502 49.050 135.560 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 0.021504 0.000000 0.000000 0.00000 SCALE2 0.000000 0.020387 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007377 0.00000