HEADER HYDROLASE 30-OCT-25 9T4C TITLE HUMAN DIPHOSPHOINOSITOL POLYPHOSPHATE PHOSPHOHYDROLASE 1 (DIPP1) H91E TITLE 2 MUTANT IN COMPLEX WITH 1,5-(PCP)-IP5 (PCP-IP8) COMPND MOL_ID: 1; COMPND 2 MOLECULE: DIPHOSPHOINOSITOL POLYPHOSPHATE PHOSPHOHYDROLASE 1; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: DIPP-1,DIADENOSINE HEXAPHOSPHATE HYDROLASE,AP6A HYDROLASE, COMPND 5 ENDOPOLYPHOSPHATASE,NUCLEOSIDE DIPHOSPHATE-LINKED MOIETY X MOTIF 3, COMPND 6 NUDIX MOTIF 3,M7GPPPN-MRNA HYDROLASE,M7GPPPX DIPHOSPHATASE; COMPND 7 EC: 3.6.1.52,3.6.1.61,3.6.1.10,3.6.1.62,3.6.1.59; COMPND 8 ENGINEERED: YES; COMPND 9 MUTATION: YES; COMPND 10 OTHER_DETAILS: DELETION OF THE LAST 24 C-TERMINAL RESIDUES (149-172), COMPND 11 THE FIRST THREE AMINO ACIDS (GHM) REMAIN AS RESIDUAL RESIDUES AFTER COMPND 12 REMOVAL OF THE EXPRESSION TAG. 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 BL21; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: STAR KEYWDS INOSITOL METABOLISM, PHOSPHATASE, NUDIX HYDROLASES, DIPP1, IP8, KEYWDS 2 HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR D.CASAS-FLOREZ,M.A.MARQUEZ-MONINO,B.GONZALEZ REVDAT 1 10-JUN-26 9T4C 0 JRNL AUTH D.CASAS-FLOREZ,H.WHITFIELD,J.M.PEREZ-CANADILLAS, JRNL AUTH 2 B.MONTERROSO,A.M.RILEY,M.A.MARQUEZ-MONINO,M.L.SHIPTON, JRNL AUTH 3 J.SANZ-APARICIO,C.A.BREARLEY,B.V.L.POTTER,B.GONZALEZ JRNL TITL THE DIPP1 FAMILY BINDS IP 8 IN CATALYTICALLY-PRODUCTIVE JRNL TITL 2 TWIST-BOAT AND CHAIR CONFORMATIONS AND ASSOCIATES IN A JRNL TITL 3 LIGAND-DEPENDENT MANNER. JRNL REF INT.J.BIOL.MACROMOL. 52715 2026 JRNL REFN ISSN 0141-8130 JRNL PMID 42202926 JRNL DOI 10.1016/J.IJBIOMAC.2026.152715 REMARK 2 REMARK 2 RESOLUTION. 1.21 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0419 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) : 1.21 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.12 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 78.3 REMARK 3 NUMBER OF REFLECTIONS : 42464 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 : NULL REMARK 3 R VALUE (WORKING + TEST SET) : NULL REMARK 3 R VALUE (WORKING SET) : 0.163 REMARK 3 FREE R VALUE : 0.189 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.011 REMARK 3 FREE R VALUE TEST SET COUNT : 2128 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) : 1.21 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.24 REMARK 3 REFLECTION IN BIN (WORKING SET) : 412 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 11.00 REMARK 3 BIN R VALUE (WORKING SET) : 0.3280 REMARK 3 BIN FREE R VALUE SET COUNT : 21 REMARK 3 BIN FREE R VALUE : 0.2970 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1186 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 56 REMARK 3 SOLVENT ATOMS : 193 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 15.50 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 18.86 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.09000 REMARK 3 B22 (A**2) : 0.00200 REMARK 3 B33 (A**2) : 0.08800 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): 0.049 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.051 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.033 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 0.779 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.972 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): 1502 ; 0.013 ; 0.012 REMARK 3 BOND LENGTHS OTHERS (A): 1340 ; 0.001 ; 0.016 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2073 ; 2.105 ; 1.902 REMARK 3 BOND ANGLES OTHERS (DEGREES): 3116 ; 0.704 ; 1.786 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 179 ; 6.832 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 14 ; 9.792 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 262 ;13.244 ;10.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 228 ; 0.106 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1755 ; 0.010 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 339 ; 0.003 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 255 ; 0.258 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 43 ; 0.190 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 586 ; 0.180 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 136 ; 0.215 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 1 ; 0.055 ; 0.200 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): 683 ; 2.012 ; 1.638 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 683 ; 2.011 ; 1.638 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 873 ; 3.024 ; 2.907 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 874 ; 3.022 ; 2.907 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 819 ; 3.678 ; 2.254 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 810 ; 3.608 ; 2.221 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1200 ; 5.800 ; 3.969 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 1195 ; 5.703 ; 3.918 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): 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 : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK BULK SOLVENT 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 THEIR REMARK 3 RIDING POSITIONS REMARK 4 REMARK 4 9T4C COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 30-OCT-25. REMARK 100 THE DEPOSITION ID IS D_1292151758. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-MAR-22 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALBA REMARK 200 BEAMLINE : XALOC REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97926 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : AUTOPROC 1.0.5 REMARK 200 DATA SCALING SOFTWARE : AUTOPROC 1.0.5 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 42464 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.210 REMARK 200 RESOLUTION RANGE LOW (A) : 50.121 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 91.3 REMARK 200 DATA REDUNDANCY : 12.30 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 15.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.21 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.30 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.400 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: FOURIER SYNTHESIS REMARK 200 SOFTWARE USED: REFMAC 5.8.0419 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.40 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.60 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PROTEIN: 20MG/ML PCP-IP8: 10MM REMARK 280 PRECIPITANT CONDITION: 26% PEG 6K, 0.1M NAOAC PH 5, 0.2M LICL, REMARK 280 1MM MNCL2 RATIO: 1:1, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE REMARK 280 289K 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 17.21150 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 39.04700 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 32.67950 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 39.04700 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 17.21150 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 32.67950 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 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 LYS A 5 REMARK 465 SER A 6 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 MN MN A 204 O HOH A 334 1.68 REMARK 500 OG SER A 40 O75 4WZ A 201 2.08 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ARG A 115 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES 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 PRO A 43 -9.77 -59.90 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 ARG A 27 0.09 SIDE CHAIN REMARK 500 ARG A 89 0.09 SIDE CHAIN REMARK 500 ARG A 115 0.07 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 ALA A 22 -13.26 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 489 DISTANCE = 6.12 ANGSTROMS REMARK 525 HOH A 490 DISTANCE = 6.20 ANGSTROMS REMARK 525 HOH A 491 DISTANCE = 6.22 ANGSTROMS REMARK 525 HOH A 492 DISTANCE = 6.29 ANGSTROMS REMARK 525 HOH A 493 DISTANCE = 6.54 ANGSTROMS REMARK 615 REMARK 615 ZERO OCCUPANCY ATOM REMARK 615 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 615 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 615 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 615 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 615 M RES C SSEQI REMARK 615 HOH A 433 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 MN A 203 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLN A 8 OE1 REMARK 620 2 GLU A 66 OE2 131.3 REMARK 620 3 4WZ A 201 O51 111.5 116.1 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN A 202 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLY A 50 O REMARK 620 2 GLU A 70 OE2 80.6 REMARK 620 3 4WZ A 201 O22 88.8 169.3 REMARK 620 4 4WZ A 201 O31 168.3 93.5 96.8 REMARK 620 5 4WZ A 201 O71 96.5 82.6 99.8 92.6 REMARK 620 6 HOH A 369 O 83.0 88.0 89.7 86.8 170.5 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN A 204 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 66 OE1 REMARK 620 2 GLU A 70 OE2 82.4 REMARK 620 3 4WZ A 201 PB1 118.3 111.6 REMARK 620 4 4WZ A 201 O71 94.9 77.7 39.6 REMARK 620 5 4WZ A 201 O51 106.5 148.6 37.5 71.7 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN A 205 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 4WZ A 201 O32 REMARK 620 2 HOH A 326 O 99.0 REMARK 620 3 HOH A 457 O 131.2 55.5 REMARK 620 N 1 2 DBREF 9T4C A 1 148 UNP O95989 NUDT3_HUMAN 1 148 SEQADV 9T4C GLU A 91 UNP O95989 HIS 91 ENGINEERED MUTATION SEQRES 1 A 148 MET MET LYS LEU LYS SER ASN GLN THR ARG THR TYR ASP SEQRES 2 A 148 GLY ASP GLY TYR LYS LYS ARG ALA ALA CYS LEU CYS PHE SEQRES 3 A 148 ARG SER GLU SER GLU GLU GLU VAL LEU LEU VAL SER SER SEQRES 4 A 148 SER ARG HIS PRO ASP ARG TRP ILE VAL PRO GLY GLY GLY SEQRES 5 A 148 MET GLU PRO GLU GLU GLU PRO SER VAL ALA ALA VAL ARG SEQRES 6 A 148 GLU VAL CYS GLU GLU ALA GLY VAL LYS GLY THR LEU GLY SEQRES 7 A 148 ARG LEU VAL GLY ILE PHE GLU ASN GLN GLU ARG LYS GLU SEQRES 8 A 148 ARG THR TYR VAL TYR VAL LEU ILE VAL THR GLU VAL LEU SEQRES 9 A 148 GLU ASP TRP GLU ASP SER VAL ASN ILE GLY ARG LYS ARG SEQRES 10 A 148 GLU TRP PHE LYS ILE GLU ASP ALA ILE LYS VAL LEU GLN SEQRES 11 A 148 TYR HIS LYS PRO VAL GLN ALA SER TYR PHE GLU THR LEU SEQRES 12 A 148 ARG GLN GLY TYR SER HET 4WZ A 201 88 HET MN A 202 1 HET MN A 203 1 HET MN A 204 1 HET MN A 205 1 HET PO4 A 206 5 HET CL A 207 1 HET CL A 208 1 HET CL A 209 1 HETNAM 4WZ {[(1R,3S,4S,5R,6S)-2,4,5,6-TETRAKIS(PHOSPHONOOXY) HETNAM 2 4WZ CYCLOHEXANE-1,3-DIYL]BIS[OXY(HYDROXYPHOSPHORYL) HETNAM 3 4WZ METHANEDIYL]}BIS(PHOSPHONIC ACID) HETNAM MN MANGANESE (II) ION HETNAM PO4 PHOSPHATE ION HETNAM CL CHLORIDE ION FORMUL 2 4WZ C8 H24 O28 P8 FORMUL 3 MN 4(MN 2+) FORMUL 7 PO4 O4 P 3- FORMUL 8 CL 3(CL 1-) FORMUL 11 HOH *193(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 TYR A 131 1 10 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 GLU A 91 VAL A 103 1 O ARG A 92 N LYS A 18 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 OE1 GLN A 8 MN MN A 203 1555 1555 2.42 LINK O GLY A 50 MN MN A 202 1555 1555 2.30 LINK OE2 GLU A 66 MN MN A 203 1555 1555 1.87 LINK OE1 GLU A 66 MN MN A 204 1555 1555 2.48 LINK OE2 GLU A 70 MN MN A 202 1555 1555 2.15 LINK OE2 GLU A 70 MN MN A 204 1555 1555 2.50 LINK O22B4WZ A 201 MN MN A 202 1555 1555 2.03 LINK O31B4WZ A 201 MN MN A 202 1555 1555 2.17 LINK O71B4WZ A 201 MN MN A 202 1555 1555 2.07 LINK O51B4WZ A 201 MN MN A 203 1555 1555 2.24 LINK PB1B4WZ A 201 MN MN A 204 1555 1555 2.37 LINK O71B4WZ A 201 MN MN A 204 1555 1555 1.87 LINK O51B4WZ A 201 MN MN A 204 1555 1555 2.39 LINK O32B4WZ A 201 MN MN A 205 1555 1555 2.18 LINK MN MN A 202 O HOH A 369 1555 1555 2.09 LINK MN MN A 205 O HOH A 326 1555 1555 1.91 LINK MN MN A 205 O HOH A 457 1555 1555 2.77 CRYST1 34.423 65.359 78.094 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 0.029050 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015300 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012805 0.00000 CONECT 57 1463 CONECT 434 1462 CONECT 574 1464 CONECT 575 1463 CONECT 613 1462 1464 CONECT 1374 1376 1384 1444 CONECT 1375 1377 1385 1445 CONECT 1376 1374 1378 1434 CONECT 1377 1375 1379 1435 CONECT 1378 1376 1380 1424 CONECT 1379 1377 1381 1425 CONECT 1380 1378 1382 1414 CONECT 1381 1379 1383 1415 CONECT 1382 1380 1384 1402 CONECT 1383 1381 1385 1403 CONECT 1384 1374 1382 1404 CONECT 1385 1375 1383 1405 CONECT 1386 1388 CONECT 1387 1389 CONECT 1388 1386 1390 1392 1394 CONECT 1389 1387 1391 1393 1395 CONECT 1390 1388 CONECT 1391 1389 CONECT 1392 1388 CONECT 1393 1389 CONECT 1394 1388 1396 CONECT 1395 1389 1397 CONECT 1396 1394 1398 1400 1402 CONECT 1397 1395 1399 1401 1403 CONECT 1398 1396 CONECT 1399 1397 CONECT 1400 1396 CONECT 1401 1397 CONECT 1402 1382 1396 CONECT 1403 1383 1397 CONECT 1404 1384 1406 CONECT 1405 1385 1407 CONECT 1406 1404 1408 1410 1412 CONECT 1407 1405 1409 1411 1413 CONECT 1408 1406 CONECT 1409 1407 CONECT 1410 1406 CONECT 1411 1407 CONECT 1412 1406 CONECT 1413 1407 CONECT 1414 1380 1416 CONECT 1415 1381 1417 CONECT 1416 1414 1418 1420 1422 CONECT 1417 1415 1419 1421 1423 CONECT 1418 1416 CONECT 1419 1417 CONECT 1420 1416 CONECT 1421 1417 CONECT 1422 1416 CONECT 1423 1417 CONECT 1424 1378 1426 CONECT 1425 1379 1427 CONECT 1426 1424 1428 1430 1432 CONECT 1427 1425 1429 1431 1433 CONECT 1428 1426 CONECT 1429 1427 CONECT 1430 1426 CONECT 1431 1427 CONECT 1432 1426 CONECT 1433 1427 CONECT 1434 1376 1436 CONECT 1435 1377 1437 CONECT 1436 1434 1438 1440 1442 CONECT 1437 1435 1439 1441 1443 CONECT 1438 1436 CONECT 1439 1437 CONECT 1440 1436 CONECT 1441 1437 1462 CONECT 1442 1436 CONECT 1443 1437 1465 CONECT 1444 1374 1446 CONECT 1445 1375 1447 CONECT 1446 1444 1448 1450 1452 CONECT 1447 1445 1449 1451 1453 CONECT 1448 1446 CONECT 1449 1447 CONECT 1450 1446 CONECT 1451 1447 1462 CONECT 1452 1446 1454 CONECT 1453 1447 1455 CONECT 1454 1452 1456 1458 1460 CONECT 1455 1453 1457 1459 1461 CONECT 1455 1464 CONECT 1456 1454 CONECT 1457 1455 CONECT 1458 1454 CONECT 1459 1455 1462 1464 CONECT 1460 1454 CONECT 1461 1455 1463 1464 CONECT 1462 434 613 1441 1451 CONECT 1462 1459 1543 CONECT 1463 57 575 1461 CONECT 1464 574 613 1455 1459 CONECT 1464 1461 CONECT 1465 1443 1499 1634 CONECT 1466 1467 1468 1469 1470 CONECT 1467 1466 CONECT 1468 1466 CONECT 1469 1466 CONECT 1470 1466 CONECT 1499 1465 CONECT 1543 1462 CONECT 1634 1465 MASTER 391 0 9 4 7 0 0 6 1435 1 108 12 END