HEADER HYDROLASE 03-JUN-13 4BR0 TITLE RAT NTPDASE2 IN COMPLEX WITH CA AMPNP COMPND MOL_ID: 1; COMPND 2 MOLECULE: ECTONUCLEOSIDE TRIPHOSPHATE DIPHOSPHOHYDROLASE 2; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 28-462; COMPND 5 SYNONYM: NTPDASE 2, CD39 ANTIGEN-LIKE 1, ECTO-ATP COMPND 6 DIPHOSPHOHYDROLASE 2, ECTO-ATPDASE 2, ECTO-ATPASE 2, NTPDASE2; COMPND 7 EC: 3.6.1.-, 3.6.1.5; COMPND 8 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, PURINERGIC SIGNALLING, DOMAIN KEYWDS 2 ROTATION, TRANSITION STATE, NTPDASE EXPDTA X-RAY DIFFRACTION AUTHOR M.ZEBISCH,P.SCHAEFER,P.LAUBLE,N.STRAETER REVDAT 3 25-DEC-13 4BR0 1 KEYWDS REVDAT 2 28-AUG-13 4BR0 1 JRNL REVDAT 1 17-JUL-13 4BR0 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, REMARK 3 STEINER,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) : 19.71 REMARK 3 DATA CUTOFF (SIGMA(F)) : NONE REMARK 3 COMPLETENESS FOR RANGE (%) : 99.66 REMARK 3 NUMBER OF REFLECTIONS : 28937 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) : 0.17077 REMARK 3 R VALUE (WORKING SET) : 0.16904 REMARK 3 FREE R VALUE : 0.21847 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 3.6 REMARK 3 FREE R VALUE TEST SET COUNT : 1071 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) : 2.050 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.103 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2074 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.31 REMARK 3 BIN R VALUE (WORKING SET) : 0.232 REMARK 3 BIN FREE R VALUE SET COUNT : 70 REMARK 3 BIN FREE R VALUE : 0.330 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 : 58 REMARK 3 SOLVENT ATOMS : 189 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 34.044 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.55 REMARK 3 B22 (A**2) : -0.43 REMARK 3 B33 (A**2) : -1.12 REMARK 3 B12 (A**2) : 0.00 REMARK 3 B13 (A**2) : 0.00 REMARK 3 B23 (A**2) : 0.00 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.171 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.158 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.099 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 6.920 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.961 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.947 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3420 ; 0.019 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4651 ; 1.987 ; 1.962 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 421 ; 6.140 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 151 ;36.554 ;23.046 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 529 ;14.514 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 24 ;17.026 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 513 ; 0.133 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2594 ; 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 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED 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): 20.2518 40.3816 9.6928 REMARK 3 T TENSOR REMARK 3 T11: 0.1923 T22: 0.0671 REMARK 3 T33: 0.0746 T12: -0.0001 REMARK 3 T13: 0.0278 T23: 0.0142 REMARK 3 L TENSOR REMARK 3 L11: 1.1301 L22: 1.6959 REMARK 3 L33: 1.8338 L12: -0.1760 REMARK 3 L13: -0.6423 L23: 0.9420 REMARK 3 S TENSOR REMARK 3 S11: 0.1256 S12: 0.1250 S13: 0.2043 REMARK 3 S21: -0.3821 S22: -0.0070 S23: -0.0472 REMARK 3 S31: -0.5700 S32: 0.0037 S33: -0.1185 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): 25.0949 26.4805 9.7885 REMARK 3 T TENSOR REMARK 3 T11: 0.0442 T22: 0.1453 REMARK 3 T33: 0.0785 T12: -0.0079 REMARK 3 T13: 0.0234 T23: -0.0274 REMARK 3 L TENSOR REMARK 3 L11: 0.9028 L22: 1.5550 REMARK 3 L33: 1.5686 L12: -0.0897 REMARK 3 L13: -0.5108 L23: 0.4895 REMARK 3 S TENSOR REMARK 3 S11: 0.0220 S12: 0.1461 S13: 0.0621 REMARK 3 S21: -0.2422 S22: 0.0339 S23: -0.0540 REMARK 3 S31: -0.1132 S32: 0.1615 S33: -0.0560 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): 26.0825 11.0428 -3.9238 REMARK 3 T TENSOR REMARK 3 T11: 0.0511 T22: 0.2210 REMARK 3 T33: 0.1301 T12: -0.0122 REMARK 3 T13: 0.0131 T23: -0.0555 REMARK 3 L TENSOR REMARK 3 L11: 2.3240 L22: 5.4038 REMARK 3 L33: 6.7744 L12: -2.1478 REMARK 3 L13: -3.8630 L23: 4.6593 REMARK 3 S TENSOR REMARK 3 S11: -0.1347 S12: 0.1914 S13: -0.0796 REMARK 3 S21: 0.1027 S22: -0.0207 S23: 0.2277 REMARK 3 S31: 0.2014 S32: -0.2812 S33: 0.1554 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): 24.5296 22.4277 30.1007 REMARK 3 T TENSOR REMARK 3 T11: 0.0363 T22: 0.1224 REMARK 3 T33: 0.0841 T12: 0.0312 REMARK 3 T13: -0.0009 T23: -0.0026 REMARK 3 L TENSOR REMARK 3 L11: 0.6427 L22: 1.1101 REMARK 3 L33: 1.7604 L12: -0.1452 REMARK 3 L13: 0.0551 L23: 0.6687 REMARK 3 S TENSOR REMARK 3 S11: -0.0685 S12: -0.0600 S13: -0.0420 REMARK 3 S21: 0.1423 S22: 0.0672 S23: -0.0812 REMARK 3 S31: 0.2078 S32: 0.1287 S33: 0.0013 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 USED IF REMARK 3 PRESENT IN THE INPUT. U VALUES WITH TLS ADDED REMARK 4 REMARK 4 4BR0 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 PDBE ID CODE IS EBI-57128. 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 : NULL REMARK 200 NUMBER OF CRYSTALS USED : NULL 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 (MX-225) REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 30057 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.05 REMARK 200 RESOLUTION RANGE LOW (A) : 36.70 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.0 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 6.3 REMARK 200 R MERGE (I) : 0.07 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 16.00 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 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 (%): 47 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.3 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM HEPES/NAOH PH 7.3, 2% REMARK 280 PEG6000, 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 20.58500 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 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 ARG A 126 NE - CZ - NH1 ANGL. DEV. = 4.3 DEGREES REMARK 500 ARG A 188 NE - CZ - NH2 ANGL. DEV. = -3.2 DEGREES REMARK 500 ARG A 387 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 THR A 122 -135.26 -115.16 REMARK 500 ARG A 188 74.26 -152.46 REMARK 500 LYS A 194 128.00 -38.60 REMARK 500 SER A 329 -84.00 -84.20 REMARK 500 PHE A 345 -164.12 -125.28 REMARK 500 SER A 346 -130.99 50.55 REMARK 500 ARG A 394 -17.93 72.40 REMARK 500 ASP A 416 -168.45 -129.12 REMARK 500 LYS A 457 19.02 49.66 REMARK 500 REMARK 500 REMARK: NULL REMARK 600 REMARK 600 HETEROGEN REMARK 600 (3S)-3-HYDROXY-1-METHYL-2,3-DIHYDRO-1H-INDOLE-5,6-DIONE REMARK 600 (AU1): AMPNP ADP 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 CA A1463 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A2070 O REMARK 620 2 HOH A2101 O 81.0 REMARK 620 3 HOH A2003 O 93.2 166.6 REMARK 620 4 HOH A2005 O 90.6 87.0 81.0 REMARK 620 5 AU1 A1462 O1A 166.5 95.6 92.7 102.3 REMARK 620 6 AU1 A1462 O2B 83.3 102.7 88.6 167.6 84.7 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 AU1 A1462 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A1463 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A1464 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A1465 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A1466 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A1467 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A1468 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: 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, REMARK 900 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, REMARK 900 APO REMARK 900 RELATED ID: 4BR9 RELATED DB: PDB REMARK 900 LEGIONELLA PNEUMOPHILA NTPDASE1 CRYSTAL FORM II, CLOSED, REMARK 900 APO REMARK 900 RELATED ID: 4BRA RELATED DB: PDB REMARK 900 LEGIONELLA PNEUMOPHILA NTPDASE1 CRYSTAL FORM II, CLOSED, REMARK 900 MG AMPPNP COMPLEX REMARK 900 RELATED ID: 4BRC RELATED DB: PDB REMARK 900 LEGIONELLA PNEUMOPHILA NTPDASE1 CRYSTAL FORM II, CLOSED, REMARK 900 MG AMPNP COMPLEX REMARK 900 RELATED ID: 4BRD RELATED DB: PDB REMARK 900 LEGIONELLA PNEUMOPHILA NTPDASE1 Q193E CRYSTAL FORM II, REMARK 900 CLOSED, MG AMPPNP COMPLEX REMARK 900 RELATED ID: 4BRE RELATED DB: PDB REMARK 900 LEGIONELLA PNEUMOPHILA NTPDASE1 CRYSTAL FORM II (CLOSED) REMARK 900 IN COMPLEX WITH TRANSITION STATE MIMIC ADENOSINE 5' REMARK 900 PHOSPHOVANADATE REMARK 900 RELATED ID: 4BRF RELATED DB: PDB REMARK 900 LEGIONELLA PNEUMOPHILA NTPDASE1 CRYSTAL FORM II (CLOSED) REMARK 900 IN COMPLEX WITH A DISTORTED ORTHOMOLYBDATE ION AND AMP REMARK 900 RELATED ID: 4BRG RELATED DB: PDB REMARK 900 LEGIONELLA PNEUMOPHILA NTPDASE1 CRYSTAL FORM II (CLOSED) REMARK 900 IN COMPLEX WITH MG GMPPNP REMARK 900 RELATED ID: 4BRH RELATED DB: PDB REMARK 900 LEGIONELLA PNEUMOPHILA NTPDASE1 CRYSTAL FORM II (CLOSED) REMARK 900 IN COMPLEX WITH MG AND THIAMINE PHOSPHOVANADATE REMARK 900 RELATED ID: 4BRI RELATED DB: PDB REMARK 900 LEGIONELLA PNEUMOPHILA NTPDASE1 CRYSTAL FORM II (CLOSED) REMARK 900 IN COMPLEX WITH MG UMPPNP REMARK 900 RELATED ID: 4BRK RELATED DB: PDB REMARK 900 LEGIONELLA PNEUMOPHILA NTPDASE1 N302Y VARIANT CRYSTAL FORM REMARK 900 III (CLOSED) IN COMPLEX WITH MG UMPPNP REMARK 900 RELATED ID: 4BRL RELATED DB: PDB REMARK 900 LEGIONELLA PNEUMOPHILA NTPDASE1 CRYSTAL FORM III (CLOSED) REMARK 900 IN COMPLEX WITH TRANSITION STATE MIMI GUANOSINE 5'- REMARK 900 PHOSPHOVANADATE REMARK 900 RELATED ID: 4BRM RELATED DB: PDB REMARK 900 SULFUR SAD PHASING OF THE LEGIONELLA PNEUMOPHILA REMARK 900 NTPDASE1 - CRYSTAL FORM III (CLOSED) IN COMPLEX WITH REMARK 900 SULFATE REMARK 900 RELATED ID: 4BRN RELATED DB: PDB REMARK 900 LEGIONELLA PNEUMOPHILA NTPDASE1 CRYSTAL FORM III (CLOSED) REMARK 900 IN COMPLEX WITH MG AMP REMARK 900 RELATED ID: 4BRO RELATED DB: PDB REMARK 900 LEGIONELLA PNEUMOPHILA NTPDASE1 CRYSTAL FORM IV (PART- REMARK 900 OPEN) REMARK 900 RELATED ID: 4BRP RELATED DB: PDB REMARK 900 LEGIONELLA PNEUMOPHILA NTPDASE1 CRYSTAL FORM V (PART- REMARK 900 OPEN) REMARK 900 RELATED ID: 4BRQ RELATED DB: PDB REMARK 900 LEGIONELLA PNEUMOPHILA NTPDASE1 CRYSTAL FORM II, CLOSED, REMARK 900 IN COMPLEX WITH TWO PHOSPHATES BOUND TO ACTIVE SITE REMARK 900 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 REMARK 900 CALCIUM AND AMPPNP DBREF 4BR0 A 28 462 UNP O35795 ENTP2_RAT 28 462 SEQADV 4BR0 MET A 6 UNP O35795 EXPRESSION TAG SEQADV 4BR0 ALA A 7 UNP O35795 EXPRESSION TAG SEQADV 4BR0 HIS A 8 UNP O35795 EXPRESSION TAG SEQADV 4BR0 HIS A 9 UNP O35795 EXPRESSION TAG SEQADV 4BR0 HIS A 10 UNP O35795 EXPRESSION TAG SEQADV 4BR0 HIS A 11 UNP O35795 EXPRESSION TAG SEQADV 4BR0 HIS A 12 UNP O35795 EXPRESSION TAG SEQADV 4BR0 HIS A 13 UNP O35795 EXPRESSION TAG SEQADV 4BR0 VAL A 14 UNP O35795 EXPRESSION TAG SEQADV 4BR0 GLY A 15 UNP O35795 EXPRESSION TAG SEQADV 4BR0 THR A 16 UNP O35795 EXPRESSION TAG SEQADV 4BR0 GLY A 17 UNP O35795 EXPRESSION TAG SEQADV 4BR0 SER A 18 UNP O35795 EXPRESSION TAG SEQADV 4BR0 ASN A 19 UNP O35795 EXPRESSION TAG SEQADV 4BR0 ASP A 20 UNP O35795 EXPRESSION TAG SEQADV 4BR0 ASP A 21 UNP O35795 EXPRESSION TAG SEQADV 4BR0 ASP A 22 UNP O35795 EXPRESSION TAG SEQADV 4BR0 ASP A 23 UNP O35795 EXPRESSION TAG SEQADV 4BR0 LYS A 24 UNP O35795 EXPRESSION TAG SEQADV 4BR0 SER A 25 UNP O35795 EXPRESSION TAG SEQADV 4BR0 PRO A 26 UNP O35795 EXPRESSION TAG SEQADV 4BR0 ASP A 27 UNP O35795 EXPRESSION TAG SEQADV 4BR0 LEU A 127 UNP O35795 PRO 127 CONFLICT SEQADV 4BR0 LEU A 128 UNP O35795 PHE 128 CONFLICT 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 AU1 A1462 27 HET CA A1463 1 HET GOL A1464 6 HET GOL A1465 6 HET GOL A1466 6 HET GOL A1467 6 HET GOL A1468 6 HETNAM AU1 5'-O-[(R)-HYDROXY(PHOSPHONOAMINO)PHOSPHORYL] HETNAM 2 AU1 ADENOSINE HETNAM CA CALCIUM ION HETNAM GOL GLYCEROL HETSYN AU1 ADENOSINE 5-(ALPHA,BETA-IMIDO)DIPHOSPHATE HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 AU1 C10 H16 N6 O9 P2 FORMUL 3 CA CA 2+ FORMUL 4 GOL 5(C3 H8 O3) FORMUL 5 HOH *189(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 SER A 95 1 7 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 ASN A 306 ARG A 316 1 11 HELIX 13 13 ALA A 347 VAL A 358 1 12 HELIX 14 14 THR A 365 GLN A 379 1 15 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 GLY A 412 1 16 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 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 2.09 SSBOND 2 CYS A 242 CYS A 284 1555 1555 2.13 SSBOND 3 CYS A 265 CYS A 310 1555 1555 2.17 SSBOND 4 CYS A 323 CYS A 328 1555 1555 2.04 SSBOND 5 CYS A 377 CYS A 399 1555 1555 2.02 LINK O1A AU1 A1462 CA CA A1463 1555 1555 2.42 LINK O2B AU1 A1462 CA CA A1463 1555 1555 2.23 LINK CA CA A1463 O HOH A2003 1555 1555 2.44 LINK CA CA A1463 O HOH A2101 1555 1555 2.33 LINK CA CA A1463 O HOH A2005 1555 1555 2.44 LINK CA CA A1463 O HOH A2070 1555 1555 2.42 CISPEP 1 ARG A 191 PRO A 192 0 -7.01 SITE 1 AC1 22 GLY A 47 SER A 48 SER A 49 HIS A 50 SITE 2 AC1 22 THR A 122 ALA A 123 GLU A 165 GLY A 203 SITE 3 AC1 22 GLY A 204 ALA A 205 SER A 206 ARG A 245 SITE 4 AC1 22 ASP A 246 TYR A 350 ARG A 394 TYR A 398 SITE 5 AC1 22 CA A1463 HOH A2046 HOH A2069 HOH A2070 SITE 6 AC1 22 HOH A2121 HOH A2124 SITE 1 AC2 5 AU1 A1462 HOH A2003 HOH A2005 HOH A2070 SITE 2 AC2 5 HOH A2101 SITE 1 AC3 7 ARG A 245 ASP A 246 ARG A 394 ASP A 397 SITE 2 AC3 7 GOL A1465 HOH A2123 HOH A2188 SITE 1 AC4 7 LEU A 249 LEU A 253 TRP A 266 ASP A 397 SITE 2 AC4 7 GOL A1464 HOH A2123 HOH A2126 SITE 1 AC5 6 PHE A 168 LEU A 228 ASN A 443 HOH A2113 SITE 2 AC5 6 HOH A2183 HOH A2189 SITE 1 AC6 5 ARG A 251 CYS A 284 GLN A 288 LEU A 317 SITE 2 AC6 5 HOH A2128 SITE 1 AC7 3 LEU A 241 CYS A 242 HOH A2141 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