HEADER HYDROLASE 30-OCT-25 9T4J TITLE HUMAN DIPHOSPHOINOSITOL POLYPHOSPHATE PHOSPHOHYDROLASE 1 (DIPP1) H91E TITLE 2 MUTANT IN COMPLEX WITH IP6 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, IP6, KEYWDS 2 HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR D.CASAS-FLOREZ,M.A.MARQUEZ-MONINO,B.GONZALEZ REVDAT 1 10-JUN-26 9T4J 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. 1.32 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) : 1.32 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.30 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 3 NUMBER OF REFLECTIONS : 41269 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) : 0.176 REMARK 3 FREE R VALUE : 0.206 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.057 REMARK 3 FREE R VALUE TEST SET COUNT : 2087 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) : 1.32 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.36 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2822 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 97.00 REMARK 3 BIN R VALUE (WORKING SET) : 0.2700 REMARK 3 BIN FREE R VALUE SET COUNT : 150 REMARK 3 BIN FREE R VALUE : 0.3320 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 : 52 REMARK 3 SOLVENT ATOMS : 183 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 17.20 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 20.10 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.11200 REMARK 3 B22 (A**2) : -0.47900 REMARK 3 B33 (A**2) : 1.59100 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): 0.054 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.057 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.039 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 0.945 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.970 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.963 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1503 ; 0.013 ; 0.012 REMARK 3 BOND LENGTHS OTHERS (A): 1351 ; 0.001 ; 0.016 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2068 ; 2.266 ; 1.894 REMARK 3 BOND ANGLES OTHERS (DEGREES): 3145 ; 0.771 ; 1.805 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 184 ; 6.794 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 15 ;10.577 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 266 ;13.075 ;10.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 201 ; 0.114 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1795 ; 0.012 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 343 ; 0.002 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 275 ; 0.216 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 50 ; 0.265 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 600 ; 0.183 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 155 ; 0.254 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 3 ; 0.165 ; 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): 691 ; 2.125 ; 1.757 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 690 ; 2.120 ; 1.757 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 890 ; 3.122 ; 3.124 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 891 ; 3.120 ; 3.123 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 812 ; 3.908 ; 2.547 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 813 ; 3.905 ; 2.551 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1178 ; 5.730 ; 4.575 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 1179 ; 5.727 ; 4.579 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 9T4J COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 31-OCT-25. REMARK 100 THE DEPOSITION ID IS D_1292151635. 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 : AIMLESS 0.7.13 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 41338 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.324 REMARK 200 RESOLUTION RANGE LOW (A) : 79.230 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 200 DATA REDUNDANCY : 12.10 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 19.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.32 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.35 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 : 2.200 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 IP6: 5MM PRECIPITANT REMARK 280 CONDITION: 26% PEG 6K 0.1M, NAOAC PH 5, 0.2M LICL RATIO: 1:1, REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 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 17.01550 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 39.61700 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 32.55300 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 39.61700 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 17.01550 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 32.55300 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 OG SER A 40 O43 IHP A 207 1.95 REMARK 500 O HOH A 434 O HOH A 454 2.01 REMARK 500 O HOH A 391 O HOH A 466 2.02 REMARK 500 O HOH A 447 O HOH A 449 2.14 REMARK 500 O2 EDO A 206 O HOH A 306 2.15 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 319 O HOH A 321 4555 2.12 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 GLU A 70 CD GLU A 70 OE2 0.066 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 MET A 2 CG - SD - CE ANGL. DEV. = 10.3 DEGREES REMARK 500 ARG A 20 NE - CZ - NH1 ANGL. DEV. = -3.6 DEGREES REMARK 500 CYS A 23 N - CA - CB ANGL. DEV. = 15.4 DEGREES REMARK 500 ARG A 45 NE - CZ - NH2 ANGL. DEV. = -3.6 DEGREES REMARK 500 ARG A 65 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 ARG A 79 NE - CZ - NH2 ANGL. DEV. = -4.5 DEGREES REMARK 500 ARG A 115 NE - CZ - NH1 ANGL. DEV. = 5.2 DEGREES REMARK 500 ARG A 115 NE - CZ - NH2 ANGL. DEV. = -3.3 DEGREES REMARK 500 ARG A 144 NE - CZ - NH1 ANGL. DEV. = -3.9 DEGREES REMARK 500 ARG A 144 NE - CZ - NH2 ANGL. DEV. = 3.2 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 HIS A 132 -20.38 -144.15 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 0.13 SIDE CHAIN REMARK 500 ARG A 41 0.09 SIDE CHAIN 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 482 DISTANCE = 6.36 ANGSTROMS REMARK 525 HOH A 483 DISTANCE = 6.41 ANGSTROMS 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 201 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLY A 50 O REMARK 620 2 GLU A 70 OE2 80.2 REMARK 620 3 SO3 A 205 O2 103.5 83.0 REMARK 620 4 IHP A 207 O23 163.0 96.3 92.5 REMARK 620 5 IHP A 207 O32 92.9 173.2 98.8 90.2 REMARK 620 6 IHP A 207 O32 95.0 175.2 97.7 88.4 2.2 REMARK 620 7 HOH A 378 O 78.5 86.9 169.1 84.7 91.7 92.8 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 202 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 66 OE1 REMARK 620 2 GLU A 70 OE2 82.3 REMARK 620 3 SO3 A 205 O2 99.2 80.3 REMARK 620 4 SO3 A 205 O3 87.6 148.9 72.4 REMARK 620 5 HOH A 311 O 78.6 110.2 168.7 96.4 REMARK 620 6 HOH A 415 O 130.3 70.0 114.8 135.4 73.9 REMARK 620 N 1 2 3 4 5 DBREF 9T4J A 1 148 UNP O95989 NUDT3_HUMAN 1 148 SEQADV 9T4J 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 MG A 201 1 HET MG A 202 1 HET CL A 203 1 HET CL A 204 1 HET SO3 A 205 4 HET EDO A 206 4 HET IHP A 207 72 HET EDO A 208 4 HETNAM MG MAGNESIUM ION HETNAM CL CHLORIDE ION HETNAM SO3 SULFITE ION HETNAM EDO 1,2-ETHANEDIOL HETNAM IHP INOSITOL HEXAKISPHOSPHATE HETSYN EDO ETHYLENE GLYCOL HETSYN IHP MYO-INOSITOL HEXAKISPHOSPHATE; INOSITOL 1,2,3,4,5,6- HETSYN 2 IHP HEXAKISPHOSPHATE FORMUL 2 MG 2(MG 2+) FORMUL 4 CL 2(CL 1-) FORMUL 6 SO3 O3 S 2- FORMUL 7 EDO 2(C2 H6 O2) FORMUL 8 IHP C6 H18 O24 P6 FORMUL 10 HOH *183(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 TYR A 96 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 201 1555 1555 2.35 LINK OE1 GLU A 66 MG MG A 202 1555 1555 2.62 LINK OE2 GLU A 70 MG MG A 201 1555 1555 2.33 LINK OE2 GLU A 70 MG MG A 202 1555 1555 2.63 LINK MG MG A 201 O2 SO3 A 205 1555 1555 2.02 LINK MG MG A 201 O23AIHP A 207 1555 1555 2.07 LINK MG MG A 201 O32AIHP A 207 1555 1555 2.38 LINK MG MG A 201 O32BIHP A 207 1555 1555 2.24 LINK MG MG A 201 O HOH A 378 1555 1555 2.21 LINK MG MG A 202 O2 SO3 A 205 1555 1555 1.73 LINK MG MG A 202 O3 SO3 A 205 1555 1555 2.24 LINK MG MG A 202 O HOH A 311 1555 1555 1.92 LINK MG MG A 202 O HOH A 415 1555 1555 2.41 CRYST1 34.031 65.106 79.234 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 0.029385 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015360 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012621 0.00000 CONECT 455 1383 CONECT 595 1384 CONECT 640 1383 1384 CONECT 1383 455 640 1389 1423 CONECT 1383 1424 1431 1554 CONECT 1384 595 640 1389 1390 CONECT 1384 1481 1594 CONECT 1387 1388 1389 1390 CONECT 1388 1387 CONECT 1389 1383 1384 1387 CONECT 1390 1384 1387 CONECT 1391 1392 1393 CONECT 1392 1391 CONECT 1393 1391 1394 CONECT 1394 1393 CONECT 1395 1397 1405 1407 CONECT 1396 1398 1406 1408 CONECT 1397 1395 1399 1417 CONECT 1398 1396 1400 1418 CONECT 1399 1397 1401 1427 CONECT 1400 1398 1402 1428 CONECT 1401 1399 1403 1437 CONECT 1402 1400 1404 1438 CONECT 1403 1401 1405 1447 CONECT 1404 1402 1406 1448 CONECT 1405 1395 1403 1457 CONECT 1406 1396 1404 1458 CONECT 1407 1395 1409 CONECT 1408 1396 1410 CONECT 1409 1407 1411 1413 1415 CONECT 1410 1408 1412 1414 1416 CONECT 1411 1409 CONECT 1412 1410 CONECT 1413 1409 CONECT 1414 1410 CONECT 1415 1409 CONECT 1416 1410 CONECT 1417 1397 1419 CONECT 1418 1398 1420 CONECT 1419 1417 1421 1423 1425 CONECT 1420 1418 1422 1424 1426 CONECT 1421 1419 CONECT 1422 1420 CONECT 1423 1383 1419 CONECT 1424 1383 1420 CONECT 1425 1419 CONECT 1426 1420 CONECT 1427 1399 1429 CONECT 1428 1400 1430 CONECT 1429 1427 1431 1433 1435 CONECT 1430 1428 1432 1434 1436 CONECT 1431 1383 1429 CONECT 1432 1430 CONECT 1433 1429 CONECT 1434 1430 CONECT 1435 1429 CONECT 1436 1430 CONECT 1437 1401 1439 CONECT 1438 1402 1440 CONECT 1439 1437 1441 1443 1445 CONECT 1440 1438 1442 1444 1446 CONECT 1441 1439 CONECT 1442 1440 CONECT 1443 1439 CONECT 1444 1440 CONECT 1445 1439 CONECT 1446 1440 CONECT 1447 1403 1449 CONECT 1448 1404 1450 CONECT 1449 1447 1451 1453 1455 CONECT 1450 1448 1452 1454 1456 CONECT 1451 1449 CONECT 1452 1450 CONECT 1453 1449 CONECT 1454 1450 CONECT 1455 1449 CONECT 1456 1450 CONECT 1457 1405 1459 CONECT 1458 1406 1460 CONECT 1459 1457 1461 1463 1465 CONECT 1460 1458 1462 1464 1466 CONECT 1461 1459 CONECT 1462 1460 CONECT 1463 1459 CONECT 1464 1460 CONECT 1465 1459 CONECT 1466 1460 CONECT 1467 1468 1469 CONECT 1468 1467 CONECT 1469 1467 1470 CONECT 1470 1469 CONECT 1481 1384 CONECT 1554 1383 CONECT 1594 1384 MASTER 400 0 8 4 7 0 0 6 1421 1 94 12 END