HEADER HYDROLASE 24-APR-20 6WOF TITLE DIPHOSPHOINOSITOL POLYPHOSPHATE PHOSPHOHYDROLASE 1 (DIPP1/NUDT3) IN TITLE 2 COMPLEX WITH INOSITOL HEXAKISPHOSPHATE AND MG, PRESOAKED WITH 5-IP7, TITLE 3 MG AND FLUORIDE, SOAKING 20MIN IN THE ABSENCE OF FLUORIDE. 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, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR G.N.ZONG,H.C.WANG,S.B.SHEARS REVDAT 2 06-MAR-24 6WOF 1 REMARK REVDAT 1 03-MAR-21 6WOF 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. 1.60 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) : 1.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 27.79 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 91.3 REMARK 3 NUMBER OF REFLECTIONS : 20415 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) : 0.124 REMARK 3 R VALUE (WORKING SET) : 0.123 REMARK 3 FREE R VALUE : 0.148 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.700 REMARK 3 FREE R VALUE TEST SET COUNT : 1008 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) : 1.60 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.64 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1096 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 67.47 REMARK 3 BIN R VALUE (WORKING SET) : 0.1040 REMARK 3 BIN FREE R VALUE SET COUNT : 49 REMARK 3 BIN FREE R VALUE : 0.1410 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1079 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 41 REMARK 3 SOLVENT ATOMS : 158 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 16.33 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.00000 REMARK 3 B22 (A**2) : 0.07000 REMARK 3 B33 (A**2) : 0.93000 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): 0.081 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.063 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.035 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.180 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.973 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.966 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1195 ; 0.007 ; 0.013 REMARK 3 BOND LENGTHS OTHERS (A): 1079 ; 0.001 ; 0.018 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 1638 ; 1.550 ; 1.689 REMARK 3 BOND ANGLES OTHERS (DEGREES): 2513 ; 1.365 ; 1.594 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 148 ; 7.201 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 70 ;27.316 ;21.429 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 209 ;12.094 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 11 ;12.271 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 154 ; 0.105 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1331 ; 0.005 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 262 ; 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): 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): 2274 ; 1.207 ; 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 10 A 602 REMARK 3 ORIGIN FOR THE GROUP (A): 5.8839 7.0629 13.7502 REMARK 3 T TENSOR REMARK 3 T11: 0.0078 T22: 0.0005 REMARK 3 T33: 0.0001 T12: -0.0004 REMARK 3 T13: 0.0003 T23: 0.0000 REMARK 3 L TENSOR REMARK 3 L11: 0.0133 L22: 0.0731 REMARK 3 L33: 0.0760 L12: -0.0244 REMARK 3 L13: 0.0013 L23: -0.0185 REMARK 3 S TENSOR REMARK 3 S11: 0.0006 S12: 0.0008 S13: -0.0001 REMARK 3 S21: -0.0003 S22: -0.0018 S23: -0.0017 REMARK 3 S31: -0.0013 S32: 0.0056 S33: 0.0011 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 6WOF 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_1000248632. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 11-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 : 22702 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.600 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 (%) : 97.3 REMARK 200 DATA REDUNDANCY : 8.800 REMARK 200 R MERGE (I) : 0.04800 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 11.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.63 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.6 REMARK 200 DATA REDUNDANCY IN SHELL : 8.90 REMARK 200 R MERGE FOR SHELL (I) : 0.23500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> 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 (%): 44.38 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 OF 200 MM LICL, 20% (W/V) PEG REMARK 280 8000, 20% (V/V) ISOPROPANOL, 100 MM HEPES, PH 7.0, 80 MM NAF, 20 REMARK 280 MM MGCL2 IN PRESENT OF 2MM 5-IP7 FOR 2 DAYS, AND TRANSFERRED REMARK 280 INTO 200 MM LICL, 20% (W/V) PEG 8000, 20% (V/V) ISOPROPANOL, 100 REMARK 280 MM HEPES, PH 7.0, 20 MM MGCL2 FOR 20 MIN., 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 23.03100 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 31.36450 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 29.91350 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 31.36450 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 23.03100 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 29.91350 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 THR A 9 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 501 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLY A 50 O REMARK 620 2 GLU A 70 OE1 84.2 REMARK 620 3 IHP A 506 O24 95.3 171.5 REMARK 620 4 IHP A 506 O25 171.5 89.8 91.6 REMARK 620 5 HOH A 612 O 97.1 80.7 90.9 87.8 REMARK 620 6 HOH A 614 O 84.9 89.4 99.1 89.0 169.6 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 502 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 66 OE2 REMARK 620 2 GLU A 70 OE1 92.5 REMARK 620 3 HOH A 612 O 86.4 79.4 REMARK 620 4 HOH A 619 O 83.9 110.4 166.4 REMARK 620 5 HOH A 680 O 169.0 83.2 102.8 88.0 REMARK 620 6 HOH A 736 O 107.7 157.9 92.8 81.2 78.4 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 503 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 IHP A 506 O34 REMARK 620 2 HOH A 601 O 120.1 REMARK 620 3 HOH A 602 O 68.6 53.9 REMARK 620 4 HOH A 612 O 78.0 94.6 99.4 REMARK 620 5 HOH A 650 O 80.2 92.5 68.3 157.7 REMARK 620 6 HOH A 695 O 91.6 146.8 147.0 102.0 82.9 REMARK 620 7 HOH A 736 O 162.0 53.2 107.1 85.8 115.2 99.3 REMARK 620 N 1 2 3 4 5 6 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 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 503 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL A 504 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL A 505 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue IHP A 506 DBREF 6WOF A 1 148 UNP O95989 NUDT3_HUMAN 1 148 SEQADV 6WOF HIS A -20 UNP O95989 EXPRESSION TAG SEQADV 6WOF HIS A -19 UNP O95989 EXPRESSION TAG SEQADV 6WOF HIS A -18 UNP O95989 EXPRESSION TAG SEQADV 6WOF HIS A -17 UNP O95989 EXPRESSION TAG SEQADV 6WOF HIS A -16 UNP O95989 EXPRESSION TAG SEQADV 6WOF HIS A -15 UNP O95989 EXPRESSION TAG SEQADV 6WOF SER A -14 UNP O95989 EXPRESSION TAG SEQADV 6WOF SER A -13 UNP O95989 EXPRESSION TAG SEQADV 6WOF GLY A -12 UNP O95989 EXPRESSION TAG SEQADV 6WOF VAL A -11 UNP O95989 EXPRESSION TAG SEQADV 6WOF ASP A -10 UNP O95989 EXPRESSION TAG SEQADV 6WOF LEU A -9 UNP O95989 EXPRESSION TAG SEQADV 6WOF GLY A -8 UNP O95989 EXPRESSION TAG SEQADV 6WOF THR A -7 UNP O95989 EXPRESSION TAG SEQADV 6WOF GLU A -6 UNP O95989 EXPRESSION TAG SEQADV 6WOF ASN A -5 UNP O95989 EXPRESSION TAG SEQADV 6WOF LEU A -4 UNP O95989 EXPRESSION TAG SEQADV 6WOF TYR A -3 UNP O95989 EXPRESSION TAG SEQADV 6WOF PHE A -2 UNP O95989 EXPRESSION TAG SEQADV 6WOF GLN A -1 UNP O95989 EXPRESSION TAG SEQADV 6WOF 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 MG A 501 1 HET MG A 502 1 HET MG A 503 1 HET CL A 504 1 HET CL A 505 1 HET IHP A 506 36 HETNAM MG MAGNESIUM ION HETNAM CL CHLORIDE ION HETNAM IHP INOSITOL HEXAKISPHOSPHATE HETSYN IHP MYO-INOSITOL HEXAKISPHOSPHATE; INOSITOL 1,2,3,4,5,6- HETSYN 2 IHP HEXAKISPHOSPHATE FORMUL 2 MG 3(MG 2+) FORMUL 5 CL 2(CL 1-) FORMUL 7 IHP C6 H18 O24 P6 FORMUL 8 HOH *158(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 501 1555 1555 2.09 LINK OE2 GLU A 66 MG MG A 502 1555 1555 2.34 LINK OE1 GLU A 70 MG MG A 501 1555 1555 2.06 LINK OE1 GLU A 70 MG MG A 502 1555 1555 2.25 LINK MG MG A 501 O24 IHP A 506 1555 1555 2.05 LINK MG MG A 501 O25 IHP A 506 1555 1555 2.06 LINK MG MG A 501 O HOH A 612 1555 1555 2.06 LINK MG MG A 501 O HOH A 614 1555 1555 2.08 LINK MG MG A 502 O HOH A 612 1555 1555 1.91 LINK MG MG A 502 O HOH A 619 1555 1555 2.03 LINK MG MG A 502 O HOH A 680 1555 1555 2.07 LINK MG MG A 502 O HOH A 736 1555 1555 2.24 LINK MG MG A 503 O34 IHP A 506 1555 1555 2.07 LINK MG MG A 503 O HOH A 601 1555 1555 2.87 LINK MG MG A 503 O HOH A 602 1555 1555 2.16 LINK MG MG A 503 O HOH A 612 1555 1555 2.05 LINK MG MG A 503 O HOH A 650 1555 1555 2.18 LINK MG MG A 503 O HOH A 695 1555 1555 2.17 LINK MG MG A 503 O HOH A 736 1555 1555 2.36 SITE 1 AC1 7 GLY A 50 GLY A 51 GLU A 70 MG A 502 SITE 2 AC1 7 IHP A 506 HOH A 612 HOH A 614 SITE 1 AC2 9 GLU A 66 GLU A 70 MG A 501 MG A 503 SITE 2 AC2 9 IHP A 506 HOH A 612 HOH A 619 HOH A 680 SITE 3 AC2 9 HOH A 736 SITE 1 AC3 8 MG A 502 IHP A 506 HOH A 601 HOH A 602 SITE 2 AC3 8 HOH A 612 HOH A 650 HOH A 695 HOH A 736 SITE 1 AC4 2 ASN A 86 GLN A 136 SITE 1 AC5 6 ARG A 27 SER A 28 SER A 30 GLU A 32 SITE 2 AC5 6 GLU A 33 HOH A 720 SITE 1 AC6 29 ARG A 10 LYS A 18 ARG A 20 SER A 39 SITE 2 AC6 29 SER A 40 ARG A 41 ILE A 47 GLY A 50 SITE 3 AC6 29 GLY A 51 GLY A 52 GLU A 70 ARG A 89 SITE 4 AC6 29 HIS A 91 ARG A 115 LYS A 133 MG A 501 SITE 5 AC6 29 MG A 502 MG A 503 HOH A 602 HOH A 612 SITE 6 AC6 29 HOH A 613 HOH A 614 HOH A 622 HOH A 632 SITE 7 AC6 29 HOH A 634 HOH A 637 HOH A 650 HOH A 680 SITE 8 AC6 29 HOH A 695 CRYST1 46.062 59.827 62.729 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 0.021710 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016715 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015942 0.00000