HEADER HYDROLASE 24-APR-20 6WOI TITLE DIPHOSPHOINOSITOL POLYPHOSPHATE PHOSPHOHYDROLASE 1 (DIPP1/NUDT3) IN TITLE 2 COMPLEX WITH 1-DIPHOSPHOINOSITOL PENTAKISPHOSPHATE, MG, AND FLUORIDE TITLE 3 ION, PRESOAKED WITH 1,5-IP8, MG AND FLUORIDE FOR 30 SECONDS 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 6WOI 1 REMARK REVDAT 1 03-MAR-21 6WOI 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. 1.50 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) : 1.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 31.63 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 90.9 REMARK 3 NUMBER OF REFLECTIONS : 24545 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) : 0.146 REMARK 3 R VALUE (WORKING SET) : 0.145 REMARK 3 FREE R VALUE : 0.167 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.800 REMARK 3 FREE R VALUE TEST SET COUNT : 1245 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) : 1.50 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.54 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1305 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 67.45 REMARK 3 BIN R VALUE (WORKING SET) : 0.1650 REMARK 3 BIN FREE R VALUE SET COUNT : 79 REMARK 3 BIN FREE R VALUE : 0.2050 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 : 131 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 17.43 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.32000 REMARK 3 B22 (A**2) : 2.33000 REMARK 3 B33 (A**2) : -3.65000 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): 0.072 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.060 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.046 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.814 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.969 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.965 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1184 ; 0.011 ; 0.013 REMARK 3 BOND LENGTHS OTHERS (A): 1067 ; 0.001 ; 0.018 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 1622 ; 1.826 ; 1.700 REMARK 3 BOND ANGLES OTHERS (DEGREES): 2483 ; 1.438 ; 1.594 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 145 ; 7.179 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 69 ;28.029 ;21.304 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 206 ;11.302 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 11 ;14.498 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 155 ; 0.131 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1299 ; 0.008 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 258 ; 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): 2251 ; 8.168 ; 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 : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 9 A 142 REMARK 3 ORIGIN FOR THE GROUP (A): 6.0818 7.2001 13.9527 REMARK 3 T TENSOR REMARK 3 T11: 0.0290 T22: 0.0047 REMARK 3 T33: 0.0371 T12: -0.0001 REMARK 3 T13: 0.0002 T23: 0.0000 REMARK 3 L TENSOR REMARK 3 L11: 0.2034 L22: 0.2226 REMARK 3 L33: 0.1104 L12: -0.0647 REMARK 3 L13: -0.0177 L23: -0.0105 REMARK 3 S TENSOR REMARK 3 S11: 0.0005 S12: 0.0092 S13: 0.0007 REMARK 3 S21: -0.0057 S22: -0.0018 S23: -0.0049 REMARK 3 S31: -0.0046 S32: 0.0205 S33: 0.0013 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 6WOI 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_1000248637. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-JUL-19 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 : APS REMARK 200 BEAMLINE : 22-ID 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 : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 28143 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.500 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 (%) : 99.0 REMARK 200 DATA REDUNDANCY : 8.400 REMARK 200 R MERGE (I) : 0.06800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.5000 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) : 1.53 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.1 REMARK 200 DATA REDUNDANCY IN SHELL : 7.30 REMARK 200 R MERGE FOR SHELL (I) : 0.56200 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 (%): 44.37 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.21 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 400 MM LICL, 30% (W/V) PEG 8000, REMARK 280 20% (V/V) ISOPROPANOL, 100MM NAAC, PH 4.5, 20 MM MGCL2 AND 80 MM REMARK 280 NAF IN PRESENT OF 2MM 1,5-IP8, AND TRANSFERRED INTO 400 MM LICL, REMARK 280 30% (W/V) PEG 8000, 20% (V/V) ISOPROPANOL, 100MM HEPES, PH 7.0, REMARK 280 20 MM MGCL2 AND 80 MM NAF FOR 30 SECOND., VAPOR DIFFUSION, REMARK 280 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 23.25150 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 31.17650 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 29.80400 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 31.17650 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 23.25150 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 29.80400 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 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 81.1 REMARK 620 3 O81 A 401 O27 100.2 84.1 REMARK 620 4 O81 A 401 O36 169.3 90.4 85.2 REMARK 620 5 O81 A 401 O21 90.9 171.0 93.4 98.0 REMARK 620 6 HOH A 562 O 86.6 91.1 170.9 87.1 92.5 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 86.2 REMARK 620 3 O81 A 401 O27 93.9 74.3 REMARK 620 4 HOH A 510 O 166.9 81.3 79.0 REMARK 620 5 HOH A 525 O 99.2 104.0 166.6 87.6 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 O81 A 401 O37 91.5 REMARK 620 3 HOH A 509 O 79.8 90.4 REMARK 620 4 HOH A 513 O 163.3 86.0 116.7 REMARK 620 5 HOH A 538 O 95.5 168.2 100.2 84.5 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 O81 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 CL 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 6WOI A 1 148 UNP O95989 NUDT3_HUMAN 1 148 SEQADV 6WOI HIS A -20 UNP O95989 EXPRESSION TAG SEQADV 6WOI HIS A -19 UNP O95989 EXPRESSION TAG SEQADV 6WOI HIS A -18 UNP O95989 EXPRESSION TAG SEQADV 6WOI HIS A -17 UNP O95989 EXPRESSION TAG SEQADV 6WOI HIS A -16 UNP O95989 EXPRESSION TAG SEQADV 6WOI HIS A -15 UNP O95989 EXPRESSION TAG SEQADV 6WOI SER A -14 UNP O95989 EXPRESSION TAG SEQADV 6WOI SER A -13 UNP O95989 EXPRESSION TAG SEQADV 6WOI GLY A -12 UNP O95989 EXPRESSION TAG SEQADV 6WOI VAL A -11 UNP O95989 EXPRESSION TAG SEQADV 6WOI ASP A -10 UNP O95989 EXPRESSION TAG SEQADV 6WOI LEU A -9 UNP O95989 EXPRESSION TAG SEQADV 6WOI GLY A -8 UNP O95989 EXPRESSION TAG SEQADV 6WOI THR A -7 UNP O95989 EXPRESSION TAG SEQADV 6WOI GLU A -6 UNP O95989 EXPRESSION TAG SEQADV 6WOI ASN A -5 UNP O95989 EXPRESSION TAG SEQADV 6WOI LEU A -4 UNP O95989 EXPRESSION TAG SEQADV 6WOI TYR A -3 UNP O95989 EXPRESSION TAG SEQADV 6WOI PHE A -2 UNP O95989 EXPRESSION TAG SEQADV 6WOI GLN A -1 UNP O95989 EXPRESSION TAG SEQADV 6WOI 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 O81 A 401 40 HET MG A 402 1 HET MG A 403 1 HET MG A 404 1 HET CL A 405 1 HET CL A 406 1 HET F A 407 1 HETNAM O81 (1S,2R,3R,4S,5S,6R)-2,3,4,5,6-PENTAKIS(PHOSPHONOOXY) HETNAM 2 O81 CYCLOHEXYL TRIHYDROGEN DIPHOSPHATE HETNAM MG MAGNESIUM ION HETNAM CL CHLORIDE ION HETNAM F FLUORIDE ION FORMUL 2 O81 C6 H19 O27 P7 FORMUL 3 MG 3(MG 2+) FORMUL 6 CL 2(CL 1-) FORMUL 8 F F 1- FORMUL 9 HOH *131(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 VAL A 100 N PHE A 26 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 2.19 LINK OE2 GLU A 66 MG MG A 403 1555 1555 2.21 LINK OE1 GLU A 66 MG MG A 404 1555 1555 2.36 LINK OE1 GLU A 70 MG MG A 402 1555 1555 2.16 LINK OE1 GLU A 70 MG MG A 403 1555 1555 2.47 LINK O27 O81 A 401 MG MG A 402 1555 1555 2.01 LINK O36 O81 A 401 MG MG A 402 1555 1555 2.24 LINK O21 O81 A 401 MG MG A 402 1555 1555 2.07 LINK O27 O81 A 401 MG MG A 403 1555 1555 2.14 LINK O37 O81 A 401 MG MG A 404 1555 1555 2.20 LINK MG MG A 402 O HOH A 562 1555 1555 1.93 LINK MG MG A 403 O HOH A 510 1555 1555 2.54 LINK MG MG A 403 O HOH A 525 1555 1555 1.86 LINK MG MG A 404 O HOH A 509 1555 1555 2.28 LINK MG MG A 404 O HOH A 513 1555 1555 2.70 LINK MG MG A 404 O HOH A 538 1555 1555 1.87 SITE 1 AC1 27 ARG A 10 LYS A 18 ARG A 20 SER A 39 SITE 2 AC1 27 SER A 40 ARG A 41 ILE A 47 GLY A 50 SITE 3 AC1 27 GLY A 51 GLY A 52 GLU A 66 GLU A 70 SITE 4 AC1 27 ARG A 89 ARG A 115 LYS A 133 MG A 402 SITE 5 AC1 27 MG A 403 MG A 404 F A 407 HOH A 501 SITE 6 AC1 27 HOH A 508 HOH A 510 HOH A 513 HOH A 535 SITE 7 AC1 27 HOH A 548 HOH A 562 HOH A 567 SITE 1 AC2 5 GLY A 50 GLU A 70 O81 A 401 MG A 403 SITE 2 AC2 5 HOH A 562 SITE 1 AC3 8 GLU A 66 GLU A 70 O81 A 401 MG A 402 SITE 2 AC3 8 MG A 404 F A 407 HOH A 510 HOH A 525 SITE 1 AC4 7 GLU A 66 O81 A 401 MG A 403 F A 407 SITE 2 AC4 7 HOH A 509 HOH A 513 HOH A 538 SITE 1 AC5 4 ASN A 86 HIS A 91 GLN A 136 HOH A 595 SITE 1 AC6 6 SER A 28 SER A 30 GLU A 31 GLU A 32 SITE 2 AC6 6 GLU A 33 HOH A 606 SITE 1 AC7 8 GLU A 66 GLU A 69 O81 A 401 MG A 403 SITE 2 AC7 8 MG A 404 HOH A 513 HOH A 525 HOH A 538 CRYST1 46.503 59.608 62.353 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 0.021504 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016776 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016038 0.00000