HEADER HYDROLASE 04-JUN-13 4BR5 TITLE RAT NTPDASE2 IN COMPLEX WITH ZN AMPPNP 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 5 20-NOV-24 4BR5 1 REMARK LINK REVDAT 4 23-AUG-17 4BR5 1 REMARK REVDAT 3 25-DEC-13 4BR5 1 KEYWDS REVDAT 2 28-AUG-13 4BR5 1 JRNL REVDAT 1 17-JUL-13 4BR5 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. 1.75 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) : 1.75 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.71 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 47078 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) : 0.170 REMARK 3 R VALUE (WORKING SET) : 0.170 REMARK 3 FREE R VALUE : 0.200 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 2.600 REMARK 3 FREE R VALUE TEST SET COUNT : 1238 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) : 1.75 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.80 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3436 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.83 REMARK 3 BIN R VALUE (WORKING SET) : 0.2790 REMARK 3 BIN FREE R VALUE SET COUNT : 91 REMARK 3 BIN FREE R VALUE : 0.3060 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3292 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 50 REMARK 3 SOLVENT ATOMS : 259 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 26.97 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.37000 REMARK 3 B22 (A**2) : 0.16000 REMARK 3 B33 (A**2) : 0.21000 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): 0.100 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.098 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.068 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 4.141 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.965 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.958 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3473 ; 0.019 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4724 ; 1.853 ; 1.961 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 434 ; 5.983 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 155 ;36.613 ;22.710 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 543 ;13.811 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 28 ;17.561 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 520 ; 0.137 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2646 ; 0.011 ; 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): 20.2884 40.3608 9.8155 REMARK 3 T TENSOR REMARK 3 T11: 0.2207 T22: 0.0901 REMARK 3 T33: 0.0305 T12: -0.0069 REMARK 3 T13: 0.0325 T23: 0.0151 REMARK 3 L TENSOR REMARK 3 L11: 1.0723 L22: 1.5355 REMARK 3 L33: 1.4750 L12: -0.0727 REMARK 3 L13: -0.6236 L23: 0.6475 REMARK 3 S TENSOR REMARK 3 S11: 0.1317 S12: 0.1061 S13: 0.1786 REMARK 3 S21: -0.3433 S22: -0.0053 S23: -0.0350 REMARK 3 S31: -0.5384 S32: 0.0357 S33: -0.1265 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): 25.1271 26.4106 9.8917 REMARK 3 T TENSOR REMARK 3 T11: 0.0719 T22: 0.1211 REMARK 3 T33: 0.0135 T12: -0.0120 REMARK 3 T13: 0.0217 T23: -0.0252 REMARK 3 L TENSOR REMARK 3 L11: 1.2633 L22: 1.6406 REMARK 3 L33: 2.0600 L12: 0.4053 REMARK 3 L13: -0.1776 L23: 0.9981 REMARK 3 S TENSOR REMARK 3 S11: 0.0276 S12: 0.0789 S13: -0.0025 REMARK 3 S21: -0.2109 S22: 0.1097 S23: -0.1015 REMARK 3 S31: -0.1318 S32: 0.1732 S33: -0.1373 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): 26.1697 11.0920 -3.9806 REMARK 3 T TENSOR REMARK 3 T11: 0.0854 T22: 0.2013 REMARK 3 T33: 0.0485 T12: 0.0025 REMARK 3 T13: 0.0174 T23: -0.0398 REMARK 3 L TENSOR REMARK 3 L11: 1.6368 L22: 3.5194 REMARK 3 L33: 5.8542 L12: -1.4031 REMARK 3 L13: -3.0596 L23: 3.1647 REMARK 3 S TENSOR REMARK 3 S11: -0.0634 S12: 0.1120 S13: -0.0189 REMARK 3 S21: -0.0971 S22: 0.0079 S23: 0.1312 REMARK 3 S31: 0.0572 S32: -0.2147 S33: 0.0555 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): 24.3449 22.3901 30.4166 REMARK 3 T TENSOR REMARK 3 T11: 0.0322 T22: 0.1094 REMARK 3 T33: 0.0120 T12: 0.0089 REMARK 3 T13: 0.0017 T23: -0.0018 REMARK 3 L TENSOR REMARK 3 L11: 0.5461 L22: 0.6007 REMARK 3 L33: 1.5341 L12: -0.0591 REMARK 3 L13: 0.1712 L23: 0.4371 REMARK 3 S TENSOR REMARK 3 S11: -0.0126 S12: -0.0371 S13: -0.0411 REMARK 3 S21: 0.0517 S22: 0.0128 S23: -0.0521 REMARK 3 S31: 0.1260 S32: 0.0824 S33: -0.0002 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 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. REMARK 4 REMARK 4 4BR5 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 04-JUN-13. REMARK 100 THE DEPOSITION ID IS D_1290057103. 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 : 5 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 : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 2M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 48382 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.750 REMARK 200 RESOLUTION RANGE LOW (A) : 19.730 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 2.000 REMARK 200 R MERGE (I) : 0.05000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 15.0000 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: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.30 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM HEPES/NAOH PH 7.3, 2% PEG6000, REMARK 280 3MM NAN3, PH 5 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 20.58500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 82.25500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 34.56500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 82.25500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 20.58500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 34.56500 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 291 REMARK 465 ALA A 292 REMARK 465 PHE A 293 REMARK 465 ASN A 294 REMARK 465 SER A 462 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 126 NE - CZ - NH1 ANGL. DEV. = 5.5 DEGREES REMARK 500 ARG A 126 NE - CZ - NH2 ANGL. DEV. = -4.9 DEGREES REMARK 500 ASP A 416 CB - CG - OD1 ANGL. DEV. = 6.6 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 THR A 122 -137.31 -123.32 REMARK 500 ARG A 188 74.97 -153.17 REMARK 500 SER A 329 -85.21 -80.87 REMARK 500 PHE A 345 -160.01 -118.01 REMARK 500 SER A 346 -129.98 44.41 REMARK 500 ARG A 394 -7.47 73.18 REMARK 500 REMARK 500 REMARK: NULL REMARK 600 REMARK 600 HETEROGEN REMARK 600 REMARK 600 PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER (ANP): AMPPNP REMARK 600 ATP ANALOG 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 ZN A1502 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ANP A1501 O2B REMARK 620 2 ANP A1501 O1G 91.6 REMARK 620 3 HOH A2004 O 85.9 97.7 REMARK 620 4 HOH A2006 O 92.6 175.7 83.2 REMARK 620 5 HOH A2095 O 173.5 82.4 92.6 93.5 REMARK 620 6 HOH A2131 O 101.4 100.2 160.4 78.3 82.0 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 ANP A 1501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 1502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 1503 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 1504 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 1505 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4BQZ RELATED DB: PDB REMARK 900 RAT NTPDASE2 IN COMPLEX WITH MG GMPPNP 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: 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 4BR5 A 28 462 UNP Q5RJP4 Q5RJP4_RAT 28 462 SEQADV 4BR5 MET A 6 UNP Q5RJP4 EXPRESSION TAG SEQADV 4BR5 ALA A 7 UNP Q5RJP4 EXPRESSION TAG SEQADV 4BR5 HIS A 8 UNP Q5RJP4 EXPRESSION TAG SEQADV 4BR5 HIS A 9 UNP Q5RJP4 EXPRESSION TAG SEQADV 4BR5 HIS A 10 UNP Q5RJP4 EXPRESSION TAG SEQADV 4BR5 HIS A 11 UNP Q5RJP4 EXPRESSION TAG SEQADV 4BR5 HIS A 12 UNP Q5RJP4 EXPRESSION TAG SEQADV 4BR5 HIS A 13 UNP Q5RJP4 EXPRESSION TAG SEQADV 4BR5 VAL A 14 UNP Q5RJP4 EXPRESSION TAG SEQADV 4BR5 GLY A 15 UNP Q5RJP4 EXPRESSION TAG SEQADV 4BR5 THR A 16 UNP Q5RJP4 EXPRESSION TAG SEQADV 4BR5 GLY A 17 UNP Q5RJP4 EXPRESSION TAG SEQADV 4BR5 SER A 18 UNP Q5RJP4 EXPRESSION TAG SEQADV 4BR5 ASN A 19 UNP Q5RJP4 EXPRESSION TAG SEQADV 4BR5 ASP A 20 UNP Q5RJP4 EXPRESSION TAG SEQADV 4BR5 ASP A 21 UNP Q5RJP4 EXPRESSION TAG SEQADV 4BR5 ASP A 22 UNP Q5RJP4 EXPRESSION TAG SEQADV 4BR5 ASP A 23 UNP Q5RJP4 EXPRESSION TAG SEQADV 4BR5 LYS A 24 UNP Q5RJP4 EXPRESSION TAG SEQADV 4BR5 SER A 25 UNP Q5RJP4 EXPRESSION TAG SEQADV 4BR5 PRO A 26 UNP Q5RJP4 EXPRESSION TAG SEQADV 4BR5 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 ANP A1501 31 HET ZN A1502 1 HET GOL A1503 6 HET GOL A1504 6 HET GOL A1505 6 HETNAM ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER HETNAM ZN ZINC ION HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 ANP C10 H17 N6 O12 P3 FORMUL 3 ZN ZN 2+ FORMUL 4 GOL 3(C3 H8 O3) FORMUL 7 HOH *259(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 GLN A 149 1 18 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 GLN A 281 1 6 HELIX 12 12 THR A 285 ARG A 289 5 5 HELIX 13 13 ASN A 306 ARG A 316 1 11 HELIX 14 14 ALA A 347 VAL A 358 1 12 HELIX 15 15 THR A 365 GLN A 379 1 15 HELIX 16 16 THR A 380 ARG A 387 1 8 HELIX 17 17 ARG A 394 ALA A 396 5 3 HELIX 18 18 ASP A 397 ARG A 411 1 15 HELIX 19 19 ASP A 416 ARG A 421 1 6 HELIX 20 20 TRP A 436 THR A 445 1 10 HELIX 21 21 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 SER A 346 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 2.06 SSBOND 2 CYS A 242 CYS A 284 1555 1555 2.10 SSBOND 3 CYS A 265 CYS A 310 1555 1555 2.13 SSBOND 4 CYS A 323 CYS A 328 1555 1555 2.09 SSBOND 5 CYS A 377 CYS A 399 1555 1555 2.02 LINK O2B ANP A1501 ZN ZN A1502 1555 1555 2.19 LINK O1G ANP A1501 ZN ZN A1502 1555 1555 2.13 LINK ZN ZN A1502 O HOH A2004 1555 1555 2.42 LINK ZN ZN A1502 O HOH A2006 1555 1555 2.34 LINK ZN ZN A1502 O HOH A2095 1555 1555 2.36 LINK ZN ZN A1502 O HOH A2131 1555 1555 2.38 CISPEP 1 ARG A 191 PRO A 192 0 -4.10 SITE 1 AC1 26 GLY A 47 SER A 48 SER A 49 HIS A 50 SITE 2 AC1 26 THR A 122 ALA A 123 GLU A 165 LEU A 202 SITE 3 AC1 26 GLY A 203 GLY A 204 ALA A 205 SER A 206 SITE 4 AC1 26 ARG A 245 ASP A 246 SER A 346 ALA A 347 SITE 5 AC1 26 TYR A 350 ARG A 394 ZN A1502 HOH A2056 SITE 6 AC1 26 HOH A2094 HOH A2095 HOH A2131 HOH A2161 SITE 7 AC1 26 HOH A2235 HOH A2256 SITE 1 AC2 5 ANP A1501 HOH A2004 HOH A2006 HOH A2095 SITE 2 AC2 5 HOH A2131 SITE 1 AC3 8 ARG A 245 ASP A 246 LEU A 249 ARG A 394 SITE 2 AC3 8 ASP A 397 HOH A2160 HOH A2161 HOH A2257 SITE 1 AC4 5 LEU A 250 TRP A 266 ASP A 397 HOH A2160 SITE 2 AC4 5 HOH A2164 SITE 1 AC5 6 PHE A 168 LEU A 228 ASN A 443 ILE A 448 SITE 2 AC5 6 HOH A2248 HOH A2250 CRYST1 41.170 69.130 164.510 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 0.024290 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014465 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006079 0.00000