HEADER HYDROLASE 03-JUN-13 4BQZ TITLE RAT NTPDASE2 IN COMPLEX WITH MG GMPPNP COMPND MOL_ID: 1; COMPND 2 MOLECULE: ECTONUCLEOSIDE TRIPHOSPHATE DIPHOSPHOHYDROLASE 2; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: ECTODOMAIN, RESIDUES 28-462; COMPND 5 SYNONYM: NTPDASE2; COMPND 6 EC: 3.6.1.5; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: RATTUS NORVEGICUS; SOURCE 3 ORGANISM_COMMON: NORWAY RAT; SOURCE 4 ORGANISM_TAXID: 10116; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS HYDROLASE, APYRASE, ATPASE, ADPASE, CD39, PURINERGIC SIGNALLING, KEYWDS 2 DOMAIN ROTATION, TRANSITION STATE, NTPDASE EXPDTA X-RAY DIFFRACTION AUTHOR M.ZEBISCH,P.SCHAEFER,P.LAUBLE,N.STRAETER REVDAT 4 06-NOV-24 4BQZ 1 REMARK LINK REVDAT 3 25-DEC-13 4BQZ 1 KEYWDS REVDAT 2 28-AUG-13 4BQZ 1 JRNL REVDAT 1 17-JUL-13 4BQZ 0 JRNL AUTH M.ZEBISCH,M.KRAUSS,P.SCHAEFER,P.LAUBLE,N.STRAETER JRNL TITL CRYSTALLOGRAPHIC SNAPSHOTS ALONG THE REACTION PATHWAY OF JRNL TITL 2 NUCLEOSIDE TRIPHOSPHATE DIPHOSPHOHYDROLASES JRNL REF STRUCTURE V. 21 1460 2013 JRNL REFN ISSN 0969-2126 JRNL PMID 23830739 JRNL DOI 10.1016/J.STR.2013.05.016 REMARK 2 REMARK 2 RESOLUTION. 2.05 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.7.0029 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) : 2.05 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 36.58 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 28778 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) : 0.185 REMARK 3 R VALUE (WORKING SET) : 0.183 REMARK 3 FREE R VALUE : 0.231 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1533 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) : 2.05 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.10 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2059 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.2600 REMARK 3 BIN FREE R VALUE SET COUNT : 114 REMARK 3 BIN FREE R VALUE : 0.3060 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3271 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 51 REMARK 3 SOLVENT ATOMS : 132 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 31.85 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.95000 REMARK 3 B22 (A**2) : 0.09000 REMARK 3 B33 (A**2) : -1.04000 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): 0.185 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.168 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.120 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 8.429 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.953 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.936 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3436 ; 0.019 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4670 ; 2.021 ; 1.962 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 425 ; 6.355 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 154 ;36.067 ;22.922 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 536 ;16.494 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 26 ;22.614 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 513 ; 0.137 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2617 ; 0.010 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL 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): 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 : 4 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 36 A 162 REMARK 3 RESIDUE RANGE : A 436 A 461 REMARK 3 ORIGIN FOR THE GROUP (A): 20.1839 40.8119 9.4712 REMARK 3 T TENSOR REMARK 3 T11: 0.2917 T22: 0.0166 REMARK 3 T33: 0.0674 T12: 0.0157 REMARK 3 T13: 0.0007 T23: 0.0246 REMARK 3 L TENSOR REMARK 3 L11: 0.8462 L22: 1.1632 REMARK 3 L33: 1.6108 L12: -0.0660 REMARK 3 L13: -0.5720 L23: 1.1109 REMARK 3 S TENSOR REMARK 3 S11: 0.0885 S12: 0.0631 S13: 0.2225 REMARK 3 S21: -0.3694 S22: -0.0100 S23: 0.0360 REMARK 3 S31: -0.5769 S32: -0.0329 S33: -0.0785 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 2 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 163 A 179 REMARK 3 RESIDUE RANGE : A 427 A 435 REMARK 3 ORIGIN FOR THE GROUP (A): 25.3071 26.8976 9.7929 REMARK 3 T TENSOR REMARK 3 T11: 0.1477 T22: 0.0394 REMARK 3 T33: 0.0299 T12: 0.0191 REMARK 3 T13: 0.0208 T23: -0.0197 REMARK 3 L TENSOR REMARK 3 L11: 2.3217 L22: 1.5063 REMARK 3 L33: 0.8363 L12: -0.2051 REMARK 3 L13: 1.1001 L23: 0.5183 REMARK 3 S TENSOR REMARK 3 S11: 0.0070 S12: 0.1047 S13: 0.0640 REMARK 3 S21: -0.1748 S22: 0.0184 S23: -0.1062 REMARK 3 S31: 0.0062 S32: 0.0972 S33: -0.0254 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 180 A 195 REMARK 3 ORIGIN FOR THE GROUP (A): 26.3754 11.3231 -3.8403 REMARK 3 T TENSOR REMARK 3 T11: 0.1316 T22: 0.1135 REMARK 3 T33: 0.1040 T12: -0.0166 REMARK 3 T13: 0.0127 T23: -0.0258 REMARK 3 L TENSOR REMARK 3 L11: 1.9957 L22: 5.0025 REMARK 3 L33: 6.6581 L12: -1.9306 REMARK 3 L13: -3.1078 L23: 5.3871 REMARK 3 S TENSOR REMARK 3 S11: -0.1794 S12: 0.0659 S13: -0.0554 REMARK 3 S21: 0.0395 S22: 0.0913 S23: 0.0964 REMARK 3 S31: 0.1780 S32: 0.0083 S33: 0.0880 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 196 A 426 REMARK 3 ORIGIN FOR THE GROUP (A): 24.7145 22.8999 30.2766 REMARK 3 T TENSOR REMARK 3 T11: 0.1335 T22: 0.0503 REMARK 3 T33: 0.0159 T12: 0.0424 REMARK 3 T13: -0.0009 T23: -0.0017 REMARK 3 L TENSOR REMARK 3 L11: 0.6275 L22: 1.3734 REMARK 3 L33: 1.2618 L12: -0.2638 REMARK 3 L13: -0.1716 L23: 0.4040 REMARK 3 S TENSOR REMARK 3 S11: -0.1007 S12: -0.0967 S13: -0.0246 REMARK 3 S21: 0.2608 S22: 0.0820 S23: -0.0892 REMARK 3 S31: 0.1757 S32: 0.1106 S33: 0.0186 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 USED IF PRESENT IN REMARK 3 THE INPUT. U VALUES WITH TLS ADDED REMARK 4 REMARK 4 4BQZ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 03-JUN-13. REMARK 100 THE DEPOSITION ID IS D_1290057127. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.3 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : BESSY REMARK 200 BEAMLINE : 14.2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9184 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 30277 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.050 REMARK 200 RESOLUTION RANGE LOW (A) : 36.600 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 3.900 REMARK 200 R MERGE (I) : 0.09000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 7.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL 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 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: OTHER REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NONE REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.72 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.31 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM HEPES/NAOH PH 7.3, 2% PEG6000, REMARK 280 3MM NAN3 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 20.44000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 81.98000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 34.88000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 81.98000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 20.44000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 34.88000 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 MET A 6 REMARK 465 ALA A 7 REMARK 465 HIS A 8 REMARK 465 HIS A 9 REMARK 465 HIS A 10 REMARK 465 HIS A 11 REMARK 465 HIS A 12 REMARK 465 HIS A 13 REMARK 465 VAL A 14 REMARK 465 GLY A 15 REMARK 465 THR A 16 REMARK 465 GLY A 17 REMARK 465 SER A 18 REMARK 465 ASN A 19 REMARK 465 ASP A 20 REMARK 465 ASP A 21 REMARK 465 ASP A 22 REMARK 465 ASP A 23 REMARK 465 LYS A 24 REMARK 465 SER A 25 REMARK 465 PRO A 26 REMARK 465 ASP A 27 REMARK 465 PRO A 28 REMARK 465 THR A 29 REMARK 465 GLN A 30 REMARK 465 ASP A 31 REMARK 465 VAL A 32 REMARK 465 ARG A 33 REMARK 465 GLU A 34 REMARK 465 PRO A 35 REMARK 465 ARG A 289 REMARK 465 PRO A 290 REMARK 465 ARG A 291 REMARK 465 ALA A 292 REMARK 465 PHE A 293 REMARK 465 ASN A 294 REMARK 465 GLY A 295 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 SER A 462 CA C O CB OG 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 ASP A 110 CB - CG - OD1 ANGL. DEV. = 6.3 DEGREES REMARK 500 ARG A 126 NE - CZ - NH1 ANGL. DEV. = 4.7 DEGREES REMARK 500 ARG A 126 NE - CZ - NH2 ANGL. DEV. = -5.2 DEGREES REMARK 500 LYS A 182 CD - CE - NZ ANGL. DEV. = -13.9 DEGREES REMARK 500 PRO A 389 C - N - CA ANGL. DEV. = -9.8 DEGREES REMARK 500 ASP A 451 CB - CG - OD1 ANGL. DEV. = 5.4 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 ASP A 88 63.08 -152.07 REMARK 500 THR A 122 -137.36 -113.96 REMARK 500 ARG A 188 73.09 -156.67 REMARK 500 CYS A 242 6.12 81.55 REMARK 500 MET A 286 -16.48 -47.23 REMARK 500 SER A 329 -86.31 -77.24 REMARK 500 PHE A 345 -159.51 -117.30 REMARK 500 SER A 346 -126.14 38.46 REMARK 500 ARG A 394 -15.36 73.18 REMARK 500 ASP A 416 -169.47 -123.38 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 A1463 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GNP A1462 O1G REMARK 620 2 GNP A1462 O2B 93.5 REMARK 620 3 HOH A2003 O 94.5 92.6 REMARK 620 4 HOH A2005 O 172.9 92.5 81.4 REMARK 620 5 HOH A2048 O 85.3 178.6 86.8 88.6 REMARK 620 6 HOH A2072 O 99.3 96.7 162.7 83.8 84.2 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GNP A 1462 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 1463 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 1464 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 1465 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 1466 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4BR0 RELATED DB: PDB REMARK 900 RAT NTPDASE2 IN COMPLEX WITH CAAMPNP REMARK 900 RELATED ID: 4BR2 RELATED DB: PDB REMARK 900 RAT NTPDASE2 IN COMPLEX WITH CA UMPPNP REMARK 900 RELATED ID: 4BR4 RELATED DB: PDB REMARK 900 LEGIONELLA PNEUMOPHILA NTPDASE1 CRYSTAL FORM I, OPEN, APO REMARK 900 RELATED ID: 4BR5 RELATED DB: PDB REMARK 900 RNNTPDASE2 IN COMPLEX WITH ZNAMPPNP REMARK 900 RELATED ID: 4BR7 RELATED DB: PDB REMARK 900 LEGIONELLA PNEUMOPHILA NTPDASE1 CRYSTAL FORM I, OPEN, APO REMARK 900 RELATED ID: 4BR9 RELATED DB: PDB REMARK 900 LEGIONELLA PNEUMOPHILA NTPDASE1 CRYSTAL FORM II, CLOSED, APO REMARK 900 RELATED ID: 4BRA RELATED DB: PDB REMARK 900 LEGIONELLA PNEUMOPHILA NTPDASE1 CRYSTAL FORM II, CLOSED, MG AMPPNP REMARK 900 COMPLEX REMARK 900 RELATED ID: 4BRC RELATED DB: PDB REMARK 900 LEGIONELLA PNEUMOPHILA NTPDASE1 CRYSTAL FORM II, CLOSED, MG AMPNP REMARK 900 COMPLEX REMARK 900 RELATED ID: 4BRD RELATED DB: PDB REMARK 900 LEGIONELLA PNEUMOPHILA NTPDASE1 Q193E CRYSTAL FORM II, CLOSED, MG REMARK 900 AMPPNP COMPLEX REMARK 900 RELATED ID: 4BRE RELATED DB: PDB REMARK 900 LEGIONELLA PNEUMOPHILA NTPDASE1 CRYSTAL FORM II (CLOSED) IN COMPLEX REMARK 900 WITH TRANSITION STATE MIMIC ADENOSINE 5' PHOSPHOVANADATE REMARK 900 RELATED ID: 4BRF RELATED DB: PDB REMARK 900 LEGIONELLA PNEUMOPHILA NTPDASE1 CRYSTAL FORM II (CLOSED) IN COMPLEX REMARK 900 WITH A DISTORTED ORTHOMOLYBDATE ION AND AMP REMARK 900 RELATED ID: 4BRG RELATED DB: PDB REMARK 900 LEGIONELLA PNEUMOPHILA NTPDASE1 CRYSTAL FORM II (CLOSED) IN COMPLEX REMARK 900 WITH MG GMPPNP REMARK 900 RELATED ID: 4BRH RELATED DB: PDB REMARK 900 LEGIONELLA PNEUMOPHILA NTPDASE1 CRYSTAL FORM II (CLOSED) IN COMPLEX REMARK 900 WITH MG AND THIAMINE PHOSPHOVANADATE REMARK 900 RELATED ID: 4BRI RELATED DB: PDB REMARK 900 LEGIONELLA PNEUMOPHILA NTPDASE1 CRYSTAL FORM II (CLOSED) IN COMPLEX REMARK 900 WITH MG UMPPNP REMARK 900 RELATED ID: 4BRK RELATED DB: PDB REMARK 900 LEGIONELLA PNEUMOPHILA NTPDASE1 N302Y VARIANT CRYSTAL FORM III REMARK 900 (CLOSED) IN COMPLEX WITH MG UMPPNP REMARK 900 RELATED ID: 4BRL RELATED DB: PDB REMARK 900 LEGIONELLA PNEUMOPHILA NTPDASE1 CRYSTAL FORM III (CLOSED) IN REMARK 900 COMPLEX WITH TRANSITION STATE MIMI GUANOSINE 5'- PHOSPHOVANADATE REMARK 900 RELATED ID: 4BRM RELATED DB: PDB REMARK 900 SULFUR SAD PHASING OF THE LEGIONELLA PNEUMOPHILA NTPDASE1 - CRYSTAL REMARK 900 FORM III (CLOSED) IN COMPLEX WITH SULFATE REMARK 900 RELATED ID: 4BRN RELATED DB: PDB REMARK 900 LEGIONELLA PNEUMOPHILA NTPDASE1 CRYSTAL FORM III (CLOSED) IN REMARK 900 COMPLEX WITH MG AMP REMARK 900 RELATED ID: 4BRO RELATED DB: PDB REMARK 900 LEGIONELLA PNEUMOPHILA NTPDASE1 CRYSTAL FORM IV (PART- OPEN) REMARK 900 RELATED ID: 4BRP RELATED DB: PDB REMARK 900 LEGIONELLA PNEUMOPHILA NTPDASE1 CRYSTAL FORM V (PART- OPEN) REMARK 900 RELATED ID: 4BRQ RELATED DB: PDB REMARK 900 LEGIONELLA PNEUMOPHILA NTPDASE1 CRYSTAL FORM II, CLOSED, IN COMPLEX REMARK 900 WITH TWO PHOSPHATES BOUND TO ACTIVE SITE MG AND PRODUCT AMP REMARK 900 RELATED ID: 3CJ1 RELATED DB: PDB REMARK 900 STRUCTURE OF RATTUS NORVEGICUS NTPDASE2 REMARK 900 RELATED ID: 3CJ7 RELATED DB: PDB REMARK 900 STRUCTURE OF RATTUS NORVEGICUS NTPDASE2 IN COMPLEX WITH AMP REMARK 900 RELATED ID: 3CJ9 RELATED DB: PDB REMARK 900 STRUCTURE OF RATTUS NORVEGICUS NTPDASE2 IN COMPLEX WITH CALCIUM, REMARK 900 AMP AND PHOSPHATE REMARK 900 RELATED ID: 3CJA RELATED DB: PDB REMARK 900 STRUCTURE OF RATTUS NORVEGICUS NTPDASE2 IN COMPLEX WITH CALCIUM AND REMARK 900 AMPPNP DBREF 4BQZ A 28 462 UNP Q5RJP4 Q5RJP4_RAT 28 462 SEQADV 4BQZ MET A 6 UNP Q5RJP4 EXPRESSION TAG SEQADV 4BQZ ALA A 7 UNP Q5RJP4 EXPRESSION TAG SEQADV 4BQZ HIS A 8 UNP Q5RJP4 EXPRESSION TAG SEQADV 4BQZ HIS A 9 UNP Q5RJP4 EXPRESSION TAG SEQADV 4BQZ HIS A 10 UNP Q5RJP4 EXPRESSION TAG SEQADV 4BQZ HIS A 11 UNP Q5RJP4 EXPRESSION TAG SEQADV 4BQZ HIS A 12 UNP Q5RJP4 EXPRESSION TAG SEQADV 4BQZ HIS A 13 UNP Q5RJP4 EXPRESSION TAG SEQADV 4BQZ VAL A 14 UNP Q5RJP4 EXPRESSION TAG SEQADV 4BQZ GLY A 15 UNP Q5RJP4 EXPRESSION TAG SEQADV 4BQZ THR A 16 UNP Q5RJP4 EXPRESSION TAG SEQADV 4BQZ GLY A 17 UNP Q5RJP4 EXPRESSION TAG SEQADV 4BQZ SER A 18 UNP Q5RJP4 EXPRESSION TAG SEQADV 4BQZ ASN A 19 UNP Q5RJP4 EXPRESSION TAG SEQADV 4BQZ ASP A 20 UNP Q5RJP4 EXPRESSION TAG SEQADV 4BQZ ASP A 21 UNP Q5RJP4 EXPRESSION TAG SEQADV 4BQZ ASP A 22 UNP Q5RJP4 EXPRESSION TAG SEQADV 4BQZ ASP A 23 UNP Q5RJP4 EXPRESSION TAG SEQADV 4BQZ LYS A 24 UNP Q5RJP4 EXPRESSION TAG SEQADV 4BQZ SER A 25 UNP Q5RJP4 EXPRESSION TAG SEQADV 4BQZ PRO A 26 UNP Q5RJP4 EXPRESSION TAG SEQADV 4BQZ ASP A 27 UNP Q5RJP4 EXPRESSION TAG SEQRES 1 A 457 MET ALA HIS HIS HIS HIS HIS HIS VAL GLY THR GLY SER SEQRES 2 A 457 ASN ASP ASP ASP ASP LYS SER PRO ASP PRO THR GLN ASP SEQRES 3 A 457 VAL ARG GLU PRO PRO ALA LEU LYS TYR GLY ILE VAL LEU SEQRES 4 A 457 ASP ALA GLY SER SER HIS THR SER MET PHE VAL TYR LYS SEQRES 5 A 457 TRP PRO ALA ASP LYS GLU ASN ASP THR GLY ILE VAL GLY SEQRES 6 A 457 GLN HIS SER SER CYS ASP VAL GLN GLY GLY GLY ILE SER SEQRES 7 A 457 SER TYR ALA ASN ASP PRO SER LYS ALA GLY GLN SER LEU SEQRES 8 A 457 VAL ARG CYS LEU GLU GLN ALA LEU ARG ASP VAL PRO ARG SEQRES 9 A 457 ASP ARG HIS ALA SER THR PRO LEU TYR LEU GLY ALA THR SEQRES 10 A 457 ALA GLY MET ARG LEU LEU ASN LEU THR SER PRO GLU ALA SEQRES 11 A 457 THR ALA ARG VAL LEU GLU ALA VAL THR GLN THR LEU THR SEQRES 12 A 457 GLN TYR PRO PHE ASP PHE ARG GLY ALA ARG ILE LEU SER SEQRES 13 A 457 GLY GLN ASP GLU GLY VAL PHE GLY TRP VAL THR ALA ASN SEQRES 14 A 457 TYR LEU LEU GLU ASN PHE ILE LYS TYR GLY TRP VAL GLY SEQRES 15 A 457 ARG TRP ILE ARG PRO ARG LYS GLY THR LEU GLY ALA MET SEQRES 16 A 457 ASP LEU GLY GLY ALA SER THR GLN ILE THR PHE GLU THR SEQRES 17 A 457 THR SER PRO SER GLU ASP PRO GLY ASN GLU VAL HIS LEU SEQRES 18 A 457 ARG LEU TYR GLY GLN HIS TYR ARG VAL TYR THR HIS SER SEQRES 19 A 457 PHE LEU CYS TYR GLY ARG ASP GLN ILE LEU LEU ARG LEU SEQRES 20 A 457 LEU ALA SER ALA LEU GLN ILE HIS ARG PHE HIS PRO CYS SEQRES 21 A 457 TRP PRO LYS GLY TYR SER THR GLN VAL LEU LEU GLN GLU SEQRES 22 A 457 VAL TYR GLN SER PRO CYS THR MET GLY GLN ARG PRO ARG SEQRES 23 A 457 ALA PHE ASN GLY SER ALA ILE VAL SER LEU SER GLY THR SEQRES 24 A 457 SER ASN ALA THR LEU CYS ARG ASP LEU VAL SER ARG LEU SEQRES 25 A 457 PHE ASN ILE SER SER CYS PRO PHE SER GLN CYS SER PHE SEQRES 26 A 457 ASN GLY VAL PHE GLN PRO PRO VAL ALA GLY ASN PHE ILE SEQRES 27 A 457 ALA PHE SER ALA PHE TYR TYR THR VAL ASP PHE LEU THR SEQRES 28 A 457 THR VAL MET GLY LEU PRO VAL GLY THR LEU LYS GLN LEU SEQRES 29 A 457 GLU GLU ALA THR GLU ILE THR CYS ASN GLN THR TRP THR SEQRES 30 A 457 GLU LEU GLN ALA ARG VAL PRO GLY GLN LYS THR ARG LEU SEQRES 31 A 457 ALA ASP TYR CYS ALA VAL ALA MET PHE ILE HIS GLN LEU SEQRES 32 A 457 LEU SER ARG GLY TYR HIS PHE ASP GLU ARG SER PHE ARG SEQRES 33 A 457 GLU VAL VAL PHE GLN LYS LYS ALA ALA ASP THR ALA VAL SEQRES 34 A 457 GLY TRP ALA LEU GLY TYR MET LEU ASN LEU THR ASN LEU SEQRES 35 A 457 ILE PRO ALA ASP LEU PRO GLY LEU ARG LYS GLY THR HIS SEQRES 36 A 457 PHE SER HET GNP A1462 32 HET MG A1463 1 HET GOL A1464 6 HET GOL A1465 6 HET GOL A1466 6 HETNAM GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER HETNAM MG MAGNESIUM ION HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 GNP C10 H17 N6 O13 P3 FORMUL 3 MG MG 2+ FORMUL 4 GOL 3(C3 H8 O3) FORMUL 7 HOH *132(H2 O) HELIX 1 1 ASP A 61 GLU A 63 5 3 HELIX 2 2 GLY A 81 ALA A 86 5 6 HELIX 3 3 PRO A 89 LEU A 96 1 8 HELIX 4 4 LEU A 96 VAL A 107 1 12 HELIX 5 5 PRO A 108 SER A 114 5 7 HELIX 6 6 THR A 122 SER A 132 1 11 HELIX 7 7 SER A 132 THR A 148 1 17 HELIX 8 8 SER A 161 LEU A 177 1 17 HELIX 9 9 ASP A 219 GLY A 221 5 3 HELIX 10 10 GLY A 244 HIS A 260 1 17 HELIX 11 11 LEU A 276 SER A 282 1 7 HELIX 12 12 ASN A 306 ARG A 316 1 11 HELIX 13 13 PHE A 345 VAL A 358 1 14 HELIX 14 14 THR A 365 ASN A 378 1 14 HELIX 15 15 THR A 380 ARG A 387 1 8 HELIX 16 16 ARG A 394 ALA A 396 5 3 HELIX 17 17 ASP A 397 ARG A 411 1 15 HELIX 18 18 ASP A 416 ARG A 421 1 6 HELIX 19 19 TRP A 436 THR A 445 1 10 HELIX 20 20 LEU A 452 THR A 459 5 8 SHEET 1 AA 5 GLY A 70 ASP A 76 0 SHEET 2 AA 5 THR A 51 PRO A 59 -1 O MET A 53 N CYS A 75 SHEET 3 AA 5 LEU A 38 ALA A 46 -1 O LYS A 39 N TRP A 58 SHEET 4 AA 5 PRO A 116 ALA A 121 1 O PRO A 116 N ILE A 42 SHEET 5 AA 5 ASP A 153 ILE A 159 1 O ASP A 153 N LEU A 117 SHEET 1 AB 2 GLY A 184 TRP A 185 0 SHEET 2 AB 2 ARG A 188 TRP A 189 -1 O ARG A 188 N TRP A 185 SHEET 1 AC 6 GLU A 223 LEU A 228 0 SHEET 2 AC 6 GLN A 231 LEU A 241 -1 O GLN A 231 N LEU A 228 SHEET 3 AC 6 SER A 206 GLU A 212 -1 O THR A 207 N PHE A 240 SHEET 4 AC 6 GLY A 198 LEU A 202 -1 O ALA A 199 N THR A 210 SHEET 5 AC 6 PHE A 342 ALA A 344 1 O ILE A 343 N MET A 200 SHEET 6 AC 6 VAL A 423 PHE A 425 1 O VAL A 424 N ALA A 344 SHEET 1 AD 2 SER A 271 LEU A 275 0 SHEET 2 AD 2 ILE A 298 SER A 302 -1 O VAL A 299 N VAL A 274 SHEET 1 AE 2 LYS A 428 ALA A 429 0 SHEET 2 AE 2 THR A 432 ALA A 433 -1 O THR A 432 N ALA A 429 SSBOND 1 CYS A 75 CYS A 99 1555 1555 2.08 SSBOND 2 CYS A 242 CYS A 284 1555 1555 2.18 SSBOND 3 CYS A 265 CYS A 310 1555 1555 2.10 SSBOND 4 CYS A 323 CYS A 328 1555 1555 2.07 SSBOND 5 CYS A 377 CYS A 399 1555 1555 1.99 LINK O1G GNP A1462 MG MG A1463 1555 1555 1.96 LINK O2B GNP A1462 MG MG A1463 1555 1555 2.02 LINK MG MG A1463 O HOH A2003 1555 1555 2.08 LINK MG MG A1463 O HOH A2005 1555 1555 2.13 LINK MG MG A1463 O HOH A2048 1555 1555 2.16 LINK MG MG A1463 O HOH A2072 1555 1555 2.12 CISPEP 1 ARG A 191 PRO A 192 0 -6.33 SITE 1 AC1 28 GLY A 47 SER A 48 SER A 49 HIS A 50 SITE 2 AC1 28 THR A 122 ALA A 123 GLU A 165 LEU A 202 SITE 3 AC1 28 GLY A 203 GLY A 204 ALA A 205 SER A 206 SITE 4 AC1 28 ARG A 245 ASP A 246 SER A 346 TYR A 350 SITE 5 AC1 28 ARG A 394 TYR A 398 MG A1463 HOH A2003 SITE 6 AC1 28 HOH A2005 HOH A2012 HOH A2029 HOH A2047 SITE 7 AC1 28 HOH A2048 HOH A2072 HOH A2109 HOH A2132 SITE 1 AC2 5 GNP A1462 HOH A2003 HOH A2005 HOH A2048 SITE 2 AC2 5 HOH A2072 SITE 1 AC3 5 LEU A 250 TRP A 266 ASP A 397 HOH A2089 SITE 2 AC3 5 HOH A2092 SITE 1 AC4 5 ASN A 179 LYS A 194 ARG A 227 ASN A 341 SITE 2 AC4 5 ASP A 451 SITE 1 AC5 6 VAL A 352 ASP A 353 THR A 356 PHE A 425 SITE 2 AC5 6 LYS A 457 HOH A2124 CRYST1 40.880 69.760 163.960 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 0.024462 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014335 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006099 0.00000