HEADER HYDROLASE 24-APR-20 6WO8 TITLE DIPHOSPHOINOSITOL POLYPHOSPHATE PHOSPHOHYDROLASE 1 (DIPP1/NUDT3) IN TITLE 2 COMPLEX WITH 5-DIPHOSPHOINOSITOL 1,3,4,6-TETRAKISPHOSPHATE (5-PP- TITLE 3 IP4), MG, AND FLUORIDE ION COMPND MOL_ID: 1; COMPND 2 MOLECULE: DIPHOSPHOINOSITOL POLYPHOSPHATE PHOSPHOHYDROLASE 1; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: DIPP-1,DIADENOSINE 5',5'''-P1,P6-HEXAPHOSPHATE HYDROLASE 1, COMPND 5 NUCLEOSIDE DIPHOSPHATE-LINKED MOIETY X MOTIF 3,NUDIX MOTIF 3; COMPND 6 EC: 3.6.1.52,3.6.1.-; 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: NUDT3, DIPP, DIPP1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS PHOSPHATASE, NUDIX, CATALYSIS MECHANISM, SUBSTRATE SPECIFICITY, KEYWDS 2 INOSITOL, INOSITOL PYROPHOSPHATE, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR G.N.ZONG,H.C.WANG,S.B.SHEARS REVDAT 2 06-MAR-24 6WO8 1 REMARK REVDAT 1 03-MAR-21 6WO8 0 JRNL AUTH G.ZONG,N.JORK,S.HOSTACHY,D.FIEDLER,H.J.JESSEN,S.B.SHEARS, JRNL AUTH 2 H.WANG JRNL TITL NEW STRUCTURAL INSIGHTS REVEAL AN EXPANDED REACTION CYCLE JRNL TITL 2 FOR INOSITOL PYROPHOSPHATE HYDROLYSIS BY HUMAN DIPP1. JRNL REF FASEB J. V. 35 21275 2021 JRNL REFN ESSN 1530-6860 JRNL PMID 33475202 JRNL DOI 10.1096/FJ.202001489R REMARK 2 REMARK 2 RESOLUTION. 1.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0253 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 43.01 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.0 REMARK 3 NUMBER OF REFLECTIONS : 17864 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.152 REMARK 3 R VALUE (WORKING SET) : 0.149 REMARK 3 FREE R VALUE : 0.216 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.700 REMARK 3 FREE R VALUE TEST SET COUNT : 882 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 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) : 1187 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 88.20 REMARK 3 BIN R VALUE (WORKING SET) : 0.1870 REMARK 3 BIN FREE R VALUE SET COUNT : 61 REMARK 3 BIN FREE R VALUE : 0.2290 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1086 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 46 REMARK 3 SOLVENT ATOMS : 159 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 22.94 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -2.66000 REMARK 3 B22 (A**2) : 2.07000 REMARK 3 B33 (A**2) : 0.59000 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): 0.121 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.103 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.091 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 6.548 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.972 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.941 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1173 ; 0.018 ; 0.013 REMARK 3 BOND LENGTHS OTHERS (A): 1063 ; 0.002 ; 0.018 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 1601 ; 2.206 ; 1.697 REMARK 3 BOND ANGLES OTHERS (DEGREES): 2469 ; 1.520 ; 1.598 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 140 ; 7.661 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 68 ;29.184 ;21.176 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 204 ;12.306 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 11 ;21.318 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 152 ; 0.165 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1274 ; 0.012 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 255 ; 0.001 ; 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): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): 2236 ;23.192 ; 3.000 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 : 1 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 2 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 9 A 142 REMARK 3 RESIDUE RANGE : A 401 A 407 REMARK 3 ORIGIN FOR THE GROUP (A): 5.987 7.134 13.876 REMARK 3 T TENSOR REMARK 3 T11: 0.0789 T22: 0.0022 REMARK 3 T33: 0.0865 T12: -0.0011 REMARK 3 T13: 0.0027 T23: -0.0005 REMARK 3 L TENSOR REMARK 3 L11: 0.2090 L22: 0.1606 REMARK 3 L33: 0.3408 L12: -0.0437 REMARK 3 L13: 0.0546 L23: -0.0187 REMARK 3 S TENSOR REMARK 3 S11: 0.0019 S12: 0.0175 S13: -0.0035 REMARK 3 S21: -0.0047 S22: -0.0028 S23: -0.0032 REMARK 3 S31: -0.0022 S32: 0.0196 S33: 0.0009 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK 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 U VALUES : WITH TLS ADDED REMARK 4 REMARK 4 6WO8 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 28-APR-20. REMARK 100 THE DEPOSITION ID IS D_1000248638. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-JUN-19 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 22-BM REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX300-HS REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 19305 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.680 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 (%) : 100.0 REMARK 200 DATA REDUNDANCY : 12.94 REMARK 200 R MERGE (I) : 0.09100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 22.0900 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.68 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.72 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.3 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.85800 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: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.90 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.19 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 10% (W/V) PEG 8000, 10% (V/V) REMARK 280 ISOPROPANOL, 200 MM LI2SO4, 75 MM NAAC, PH 5.5 AND 25 MM HEPES, REMARK 280 PH 7.0 AND SOAKING IN SOLUTION OF 200 MM LICL, 20% (W/V) PEG REMARK 280 8000, 20% (V/V) ISOPROPANOL, 100 MM HEPES, PH 7.0, 20 MM MGCL2 REMARK 280 AND 80 MM NAF IN PRESENT OF 2MM 5-PP-IP4, PH 6.0, VAPOR REMARK 280 DIFFUSION, HANGING DROP, 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 23.14000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 31.13000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 29.74000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 31.13000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 23.14000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 29.74000 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 HIS A -20 REMARK 465 HIS A -19 REMARK 465 HIS A -18 REMARK 465 HIS A -17 REMARK 465 HIS A -16 REMARK 465 HIS A -15 REMARK 465 SER A -14 REMARK 465 SER A -13 REMARK 465 GLY A -12 REMARK 465 VAL A -11 REMARK 465 ASP A -10 REMARK 465 LEU A -9 REMARK 465 GLY A -8 REMARK 465 THR A -7 REMARK 465 GLU A -6 REMARK 465 ASN A -5 REMARK 465 LEU A -4 REMARK 465 TYR A -3 REMARK 465 PHE A -2 REMARK 465 GLN A -1 REMARK 465 SER A 0 REMARK 465 MET A 1 REMARK 465 MET A 2 REMARK 465 LYS A 3 REMARK 465 LEU A 4 REMARK 465 LYS A 5 REMARK 465 SER A 6 REMARK 465 ASN A 7 REMARK 465 GLN A 8 REMARK 465 LEU A 143 REMARK 465 ARG A 144 REMARK 465 GLN A 145 REMARK 465 GLY A 146 REMARK 465 TYR A 147 REMARK 465 SER A 148 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 56 15.35 55.50 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 A 402 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLY A 50 O REMARK 620 2 GLU A 70 OE1 82.2 REMARK 620 3 U6J A 401 O44 165.1 91.0 REMARK 620 4 U6J A 401 O35 92.8 171.6 95.3 REMARK 620 5 U6J A 401 O55 102.4 81.2 89.6 93.3 REMARK 620 6 HOH A 506 O 79.4 88.3 87.2 97.5 168.9 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 403 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 66 OE2 REMARK 620 2 GLU A 70 OE1 90.5 REMARK 620 3 U6J A 401 O55 92.2 74.4 REMARK 620 4 HOH A 563 O 85.0 107.6 176.6 REMARK 620 5 HOH A 578 O 176.4 86.4 88.7 94.1 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 404 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 66 OE1 REMARK 620 2 U6J A 401 O65 92.6 REMARK 620 3 HOH A 530 O 80.8 91.7 REMARK 620 4 HOH A 554 O 85.5 169.1 98.5 REMARK 620 5 HOH A 611 O 169.1 93.6 90.0 90.2 REMARK 620 N 1 2 3 4 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue U6J A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 404 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL A 405 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 406 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue F A 407 DBREF 6WO8 A 1 148 UNP O95989 NUDT3_HUMAN 1 148 SEQADV 6WO8 HIS A -20 UNP O95989 EXPRESSION TAG SEQADV 6WO8 HIS A -19 UNP O95989 EXPRESSION TAG SEQADV 6WO8 HIS A -18 UNP O95989 EXPRESSION TAG SEQADV 6WO8 HIS A -17 UNP O95989 EXPRESSION TAG SEQADV 6WO8 HIS A -16 UNP O95989 EXPRESSION TAG SEQADV 6WO8 HIS A -15 UNP O95989 EXPRESSION TAG SEQADV 6WO8 SER A -14 UNP O95989 EXPRESSION TAG SEQADV 6WO8 SER A -13 UNP O95989 EXPRESSION TAG SEQADV 6WO8 GLY A -12 UNP O95989 EXPRESSION TAG SEQADV 6WO8 VAL A -11 UNP O95989 EXPRESSION TAG SEQADV 6WO8 ASP A -10 UNP O95989 EXPRESSION TAG SEQADV 6WO8 LEU A -9 UNP O95989 EXPRESSION TAG SEQADV 6WO8 GLY A -8 UNP O95989 EXPRESSION TAG SEQADV 6WO8 THR A -7 UNP O95989 EXPRESSION TAG SEQADV 6WO8 GLU A -6 UNP O95989 EXPRESSION TAG SEQADV 6WO8 ASN A -5 UNP O95989 EXPRESSION TAG SEQADV 6WO8 LEU A -4 UNP O95989 EXPRESSION TAG SEQADV 6WO8 TYR A -3 UNP O95989 EXPRESSION TAG SEQADV 6WO8 PHE A -2 UNP O95989 EXPRESSION TAG SEQADV 6WO8 GLN A -1 UNP O95989 EXPRESSION TAG SEQADV 6WO8 SER A 0 UNP O95989 EXPRESSION TAG SEQRES 1 A 169 HIS HIS HIS HIS HIS HIS SER SER GLY VAL ASP LEU GLY SEQRES 2 A 169 THR GLU ASN LEU TYR PHE GLN SER MET MET LYS LEU LYS SEQRES 3 A 169 SER ASN GLN THR ARG THR TYR ASP GLY ASP GLY TYR LYS SEQRES 4 A 169 LYS ARG ALA ALA CYS LEU CYS PHE ARG SER GLU SER GLU SEQRES 5 A 169 GLU GLU VAL LEU LEU VAL SER SER SER ARG HIS PRO ASP SEQRES 6 A 169 ARG TRP ILE VAL PRO GLY GLY GLY MET GLU PRO GLU GLU SEQRES 7 A 169 GLU PRO SER VAL ALA ALA VAL ARG GLU VAL CYS GLU GLU SEQRES 8 A 169 ALA GLY VAL LYS GLY THR LEU GLY ARG LEU VAL GLY ILE SEQRES 9 A 169 PHE GLU ASN GLN GLU ARG LYS HIS ARG THR TYR VAL TYR SEQRES 10 A 169 VAL LEU ILE VAL THR GLU VAL LEU GLU ASP TRP GLU ASP SEQRES 11 A 169 SER VAL ASN ILE GLY ARG LYS ARG GLU TRP PHE LYS ILE SEQRES 12 A 169 GLU ASP ALA ILE LYS VAL LEU GLN TYR HIS LYS PRO VAL SEQRES 13 A 169 GLN ALA SER TYR PHE GLU THR LEU ARG GLN GLY TYR SER HET U6J A 401 36 HET MG A 402 1 HET MG A 403 1 HET MG A 404 1 HET CL A 405 1 HET SO4 A 406 5 HET F A 407 1 HETNAM U6J (1R,2R,3S,4R,5R,6S)-4-HYDROXY-2,3,5,6- HETNAM 2 U6J TETRAKIS(PHOSPHONOOXY)CYCLOHEXYL TRIHYDROGEN HETNAM 3 U6J DIPHOSPHATE HETNAM MG MAGNESIUM ION HETNAM CL CHLORIDE ION HETNAM SO4 SULFATE ION HETNAM F FLUORIDE ION FORMUL 2 U6J C6 H18 O24 P6 FORMUL 3 MG 3(MG 2+) FORMUL 6 CL CL 1- FORMUL 7 SO4 O4 S 2- FORMUL 8 F F 1- FORMUL 9 HOH *159(H2 O) HELIX 1 AA1 GLU A 58 GLY A 72 1 15 HELIX 2 AA2 TRP A 107 GLY A 114 1 8 HELIX 3 AA3 ILE A 122 GLN A 130 1 9 HELIX 4 AA4 LYS A 133 TYR A 139 1 7 SHEET 1 AA1 4 GLY A 50 GLY A 52 0 SHEET 2 AA1 4 LYS A 18 PHE A 26 -1 N ALA A 21 O GLY A 51 SHEET 3 AA1 4 HIS A 91 VAL A 103 1 O LEU A 98 N LEU A 24 SHEET 4 AA1 4 VAL A 73 ASN A 86 -1 N GLY A 78 O VAL A 97 SHEET 1 AA2 3 TRP A 46 ILE A 47 0 SHEET 2 AA2 3 GLU A 33 SER A 38 -1 N VAL A 37 O ILE A 47 SHEET 3 AA2 3 ARG A 117 LYS A 121 -1 O PHE A 120 N VAL A 34 LINK O GLY A 50 MG MG A 402 1555 1555 1.99 LINK OE2 GLU A 66 MG MG A 403 1555 1555 2.21 LINK OE1 GLU A 66 MG MG A 404 1555 1555 2.20 LINK OE1 GLU A 70 MG MG A 402 1555 1555 2.01 LINK OE1 GLU A 70 MG MG A 403 1555 1555 2.19 LINK O44 U6J A 401 MG MG A 402 1555 1555 1.97 LINK O35 U6J A 401 MG MG A 402 1555 1555 2.03 LINK O55 U6J A 401 MG MG A 402 1555 1555 1.95 LINK O55 U6J A 401 MG MG A 403 1555 1555 2.08 LINK O65 U6J A 401 MG MG A 404 1555 1555 2.04 LINK MG MG A 402 O HOH A 506 1555 1555 2.11 LINK MG MG A 403 O HOH A 563 1555 1555 2.06 LINK MG MG A 403 O HOH A 578 1555 1555 2.19 LINK MG MG A 404 O HOH A 530 1555 1555 2.07 LINK MG MG A 404 O HOH A 554 1555 1555 1.97 LINK MG MG A 404 O HOH A 611 1555 1555 2.20 SITE 1 AC1 32 ARG A 10 LYS A 18 ARG A 20 SER A 39 SITE 2 AC1 32 SER A 40 ARG A 41 ILE A 47 GLY A 50 SITE 3 AC1 32 GLY A 51 GLY A 52 GLU A 66 GLU A 70 SITE 4 AC1 32 ARG A 89 HIS A 91 ARG A 115 LYS A 133 SITE 5 AC1 32 MG A 402 MG A 403 MG A 404 F A 407 SITE 6 AC1 32 HOH A 505 HOH A 506 HOH A 511 HOH A 530 SITE 7 AC1 32 HOH A 532 HOH A 535 HOH A 544 HOH A 568 SITE 8 AC1 32 HOH A 578 HOH A 581 HOH A 587 HOH A 611 SITE 1 AC2 6 GLY A 50 GLY A 51 GLU A 70 U6J A 401 SITE 2 AC2 6 MG A 403 HOH A 506 SITE 1 AC3 8 GLU A 66 GLU A 70 U6J A 401 MG A 402 SITE 2 AC3 8 MG A 404 F A 407 HOH A 563 HOH A 578 SITE 1 AC4 7 GLU A 66 U6J A 401 MG A 403 F A 407 SITE 2 AC4 7 HOH A 530 HOH A 554 HOH A 611 SITE 1 AC5 6 SER A 28 SER A 30 GLU A 31 GLU A 32 SITE 2 AC5 6 GLU A 33 HOH A 615 SITE 1 AC6 8 ARG A 20 ASN A 86 HIS A 91 VAL A 135 SITE 2 AC6 8 GLN A 136 TYR A 139 HOH A 528 HOH A 582 SITE 1 AC7 10 GLU A 66 U6J A 401 MG A 403 MG A 404 SITE 2 AC7 10 HOH A 505 HOH A 554 HOH A 563 HOH A 578 SITE 3 AC7 10 HOH A 611 HOH A 644 CRYST1 46.280 59.480 62.260 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 0.021608 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016812 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016062 0.00000