HEADER HYDROLASE 04-JUN-13 4BR9 TITLE LEGIONELLA PNEUMOPHILA NTPDASE1 CRYSTAL FORM II, CLOSED, APO COMPND MOL_ID: 1; COMPND 2 MOLECULE: ECTONUCLEOSIDE TRIPHOSPHATE DIPHOSPHOHYDROLASE I; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: RESIDUES 35-393; COMPND 5 SYNONYM: NTPDASE1; COMPND 6 EC: 3.6.1.5; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: LEGIONELLA PNEUMOPHILA; SOURCE 3 ORGANISM_TAXID: 446; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 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 6 13-NOV-24 4BR9 1 REMARK REVDAT 5 23-AUG-17 4BR9 1 REMARK REVDAT 4 25-DEC-13 4BR9 1 KEYWDS REVDAT 3 02-OCT-13 4BR9 1 MTRIX1 MTRIX2 MTRIX3 REVDAT 2 28-AUG-13 4BR9 1 JRNL REVDAT 1 17-JUL-13 4BR9 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. 1.40 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) : 1.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.20 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 96.1 REMARK 3 NUMBER OF REFLECTIONS : 136028 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) : 0.128 REMARK 3 R VALUE (WORKING SET) : 0.127 REMARK 3 FREE R VALUE : 0.171 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 1.500 REMARK 3 FREE R VALUE TEST SET COUNT : 2070 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) : 1.40 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.44 REMARK 3 REFLECTION IN BIN (WORKING SET) : 7073 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 67.74 REMARK 3 BIN R VALUE (WORKING SET) : 0.2050 REMARK 3 BIN FREE R VALUE SET COUNT : 106 REMARK 3 BIN FREE R VALUE : 0.2560 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5771 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 26 REMARK 3 SOLVENT ATOMS : 648 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 20.84 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.53000 REMARK 3 B22 (A**2) : 0.13000 REMARK 3 B33 (A**2) : -0.62000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.25000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.055 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.054 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.031 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.690 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.978 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.961 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 6340 ; 0.020 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 8744 ; 1.957 ; 1.943 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 840 ; 6.120 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 327 ;43.259 ;26.269 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1050 ;12.509 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 9 ; 9.745 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 951 ; 0.129 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 5007 ; 0.013 ; 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): 6340 ; 6.399 ; 3.000 REMARK 3 SPHERICITY; FREE ATOMS (A**2): 163 ;32.599 ; 5.000 REMARK 3 SPHERICITY; BONDED ATOMS (A**2): 6613 ;19.285 ; 5.000 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 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 THE RIDING REMARK 3 POSITIONS. REMARK 4 REMARK 4 4BR9 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_1290057137. 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 : 5.5 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) : 1.2144 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 : 138132 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.400 REMARK 200 RESOLUTION RANGE LOW (A) : 29.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.2 REMARK 200 DATA REDUNDANCY : 4.500 REMARK 200 R MERGE (I) : 0.04000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 21.0000 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 (%): 44.50 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.20 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 9% PEG3350, 100MM (NH4)2SO4, 100MM REMARK 280 NAMES PH 5.5 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 43.09900 REMARK 290 SMTRY3 2 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4850 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 29010 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -131.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 GLU A 395 REMARK 465 HIS A 396 REMARK 465 HIS A 397 REMARK 465 HIS A 398 REMARK 465 HIS A 399 REMARK 465 HIS A 400 REMARK 465 HIS A 401 REMARK 465 HIS B 396 REMARK 465 HIS B 397 REMARK 465 HIS B 398 REMARK 465 HIS B 399 REMARK 465 HIS B 400 REMARK 465 HIS B 401 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 OE1 GLN A 283 O HOH A 2272 1.42 REMARK 500 OG SER A 305 O HOH A 2298 2.12 REMARK 500 O1 GOL A 1396 O HOH A 2364 2.14 REMARK 500 CD GLN A 283 O HOH A 2272 2.15 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 LEU B 227 N LEU B 227 CA -0.138 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ARG A 122 NE - CZ - NH2 ANGL. DEV. = -3.3 DEGREES REMARK 500 ARG B 122 NE - CZ - NH1 ANGL. DEV. = 5.1 DEGREES REMARK 500 LYS B 152 CD - CE - NZ ANGL. DEV. = 14.8 DEGREES REMARK 500 ASP B 158 CB - CG - OD1 ANGL. DEV. = -6.0 DEGREES REMARK 500 LEU B 212 CB - CG - CD1 ANGL. DEV. = -10.5 DEGREES REMARK 500 PHE B 226 CA - C - N ANGL. DEV. = -16.4 DEGREES REMARK 500 PHE B 226 O - C - N ANGL. DEV. = 14.9 DEGREES REMARK 500 ARG B 392 NE - CZ - NH2 ANGL. DEV. = -3.3 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 118 -122.58 -124.42 REMARK 500 GLN A 258 78.10 -152.78 REMARK 500 VAL A 275 -66.98 -91.29 REMARK 500 ILE A 329 -58.48 -127.98 REMARK 500 ASP A 383 -165.82 -121.13 REMARK 500 HIS B 109 -157.27 -141.16 REMARK 500 THR B 118 -131.20 -125.05 REMARK 500 LEU B 229 2.05 -59.59 REMARK 500 GLN B 258 75.84 -152.44 REMARK 500 ILE B 329 -58.37 -130.22 REMARK 500 ASP B 383 -168.43 -123.70 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 1395 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 1396 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 1396 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 1397 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 1397 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: 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: 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 4BR9 A 35 393 UNP Q5ZUA2 Q5ZUA2_LEGPH 35 393 DBREF 4BR9 B 35 393 UNP Q5ZUA2 Q5ZUA2_LEGPH 35 393 SEQADV 4BR9 MET A 34 UNP Q5ZUA2 EXPRESSION TAG SEQADV 4BR9 LEU A 394 UNP Q5ZUA2 EXPRESSION TAG SEQADV 4BR9 GLU A 395 UNP Q5ZUA2 EXPRESSION TAG SEQADV 4BR9 HIS A 396 UNP Q5ZUA2 EXPRESSION TAG SEQADV 4BR9 HIS A 397 UNP Q5ZUA2 EXPRESSION TAG SEQADV 4BR9 HIS A 398 UNP Q5ZUA2 EXPRESSION TAG SEQADV 4BR9 HIS A 399 UNP Q5ZUA2 EXPRESSION TAG SEQADV 4BR9 HIS A 400 UNP Q5ZUA2 EXPRESSION TAG SEQADV 4BR9 HIS A 401 UNP Q5ZUA2 EXPRESSION TAG SEQADV 4BR9 ASP A 137 UNP Q5ZUA2 GLU 137 CONFLICT SEQADV 4BR9 VAL A 149 UNP Q5ZUA2 ALA 149 CONFLICT SEQADV 4BR9 MET B 34 UNP Q5ZUA2 EXPRESSION TAG SEQADV 4BR9 LEU B 394 UNP Q5ZUA2 EXPRESSION TAG SEQADV 4BR9 GLU B 395 UNP Q5ZUA2 EXPRESSION TAG SEQADV 4BR9 HIS B 396 UNP Q5ZUA2 EXPRESSION TAG SEQADV 4BR9 HIS B 397 UNP Q5ZUA2 EXPRESSION TAG SEQADV 4BR9 HIS B 398 UNP Q5ZUA2 EXPRESSION TAG SEQADV 4BR9 HIS B 399 UNP Q5ZUA2 EXPRESSION TAG SEQADV 4BR9 HIS B 400 UNP Q5ZUA2 EXPRESSION TAG SEQADV 4BR9 HIS B 401 UNP Q5ZUA2 EXPRESSION TAG SEQADV 4BR9 ASP B 137 UNP Q5ZUA2 GLU 137 CONFLICT SEQADV 4BR9 VAL B 149 UNP Q5ZUA2 ALA 149 CONFLICT SEQRES 1 A 368 MET ASP THR ASN PRO CYS GLU LYS HIS SER CYS ILE ALA SEQRES 2 A 368 VAL ILE ASP ALA GLY SER THR GLY SER ARG LEU HIS ILE SEQRES 3 A 368 TYR SER TYR ASP THR ASP ASP THR ASN THR PRO ILE HIS SEQRES 4 A 368 ILE GLU GLU ILE TRP ASN LYS LYS ILE LYS PRO GLY PHE SEQRES 5 A 368 ALA SER ILE GLN PRO ASN SER VAL THR ILE ASP ALA TYR SEQRES 6 A 368 LEU THR MET LEU LEU ALA ASP ALA PRO ILE HIS ASN ILE SEQRES 7 A 368 PRO VAL TYR PHE TYR ALA THR ALA GLY MET ARG LEU LEU SEQRES 8 A 368 PRO GLN SER GLN GLN LYS LYS TYR TYR ASP GLU LEU ASP SEQRES 9 A 368 TYR TRP PHE ARG GLN GLN SER GLN TRP GLN LEU VAL GLU SEQRES 10 A 368 ALA LYS THR ILE THR GLY ASN ASP GLU ALA LEU PHE ASP SEQRES 11 A 368 TRP LEU ALA VAL ASN TYR LYS LEU ASP THR LEU LYS SER SEQRES 12 A 368 VAL GLN ASN LYS SER VAL GLY VAL MET ASP MET GLY GLY SEQRES 13 A 368 ALA SER VAL GLN ILE VAL PHE PRO MET PRO LYS ASN ALA SEQRES 14 A 368 GLU ILE SER LYS HIS ASN GLN VAL GLU LEU ASN ILE TYR SEQRES 15 A 368 GLY GLN ASN ILE ASN LEU TYR VAL HIS SER PHE LEU GLY SEQRES 16 A 368 LEU GLY GLN THR GLU MET SER HIS GLN PHE LEU ASN SER SEQRES 17 A 368 PRO SER CYS PHE ALA ASN ASP TYR PRO LEU PRO ASP GLY SEQRES 18 A 368 GLU SER GLY GLN GLY ASN ALA PRO SER CYS LYS GLU GLU SEQRES 19 A 368 VAL THR SER LEU MET ASN SER VAL HIS LYS VAL ASN GLN SEQRES 20 A 368 GLN ILE GLN PRO LEU LEU ALA LEU ASN PRO VAL ASN GLU SEQRES 21 A 368 TRP TYR SER ILE GLY GLY ILE SER ASN LEU ALA SER SER SEQRES 22 A 368 GLN LEU PHE HIS PHE GLU ASN SER GLU LEU THR ASN GLN SEQRES 23 A 368 SER LEU LEU GLN GLN GLY ASP ASN GLN ILE CYS HIS GLN SEQRES 24 A 368 GLN TRP ASP ILE LEU ASN GLY GLN TYR PRO ASP ASP GLU SEQRES 25 A 368 TYR LEU TYR GLN TYR CYS LEU LEU SER SER TYR TYR TYR SEQRES 26 A 368 ALA LEU MET VAL ASP GLY TYR GLY ILE ASN PRO ASN GLN SEQRES 27 A 368 THR ILE HIS TYR ILE PRO PRO GLU GLN ASN LEU ASP TRP SEQRES 28 A 368 THR ILE GLY VAL VAL LEU HIS ARG ALA LEU GLU HIS HIS SEQRES 29 A 368 HIS HIS HIS HIS SEQRES 1 B 368 MET ASP THR ASN PRO CYS GLU LYS HIS SER CYS ILE ALA SEQRES 2 B 368 VAL ILE ASP ALA GLY SER THR GLY SER ARG LEU HIS ILE SEQRES 3 B 368 TYR SER TYR ASP THR ASP ASP THR ASN THR PRO ILE HIS SEQRES 4 B 368 ILE GLU GLU ILE TRP ASN LYS LYS ILE LYS PRO GLY PHE SEQRES 5 B 368 ALA SER ILE GLN PRO ASN SER VAL THR ILE ASP ALA TYR SEQRES 6 B 368 LEU THR MET LEU LEU ALA ASP ALA PRO ILE HIS ASN ILE SEQRES 7 B 368 PRO VAL TYR PHE TYR ALA THR ALA GLY MET ARG LEU LEU SEQRES 8 B 368 PRO GLN SER GLN GLN LYS LYS TYR TYR ASP GLU LEU ASP SEQRES 9 B 368 TYR TRP PHE ARG GLN GLN SER GLN TRP GLN LEU VAL GLU SEQRES 10 B 368 ALA LYS THR ILE THR GLY ASN ASP GLU ALA LEU PHE ASP SEQRES 11 B 368 TRP LEU ALA VAL ASN TYR LYS LEU ASP THR LEU LYS SER SEQRES 12 B 368 VAL GLN ASN LYS SER VAL GLY VAL MET ASP MET GLY GLY SEQRES 13 B 368 ALA SER VAL GLN ILE VAL PHE PRO MET PRO LYS ASN ALA SEQRES 14 B 368 GLU ILE SER LYS HIS ASN GLN VAL GLU LEU ASN ILE TYR SEQRES 15 B 368 GLY GLN ASN ILE ASN LEU TYR VAL HIS SER PHE LEU GLY SEQRES 16 B 368 LEU GLY GLN THR GLU MET SER HIS GLN PHE LEU ASN SER SEQRES 17 B 368 PRO SER CYS PHE ALA ASN ASP TYR PRO LEU PRO ASP GLY SEQRES 18 B 368 GLU SER GLY GLN GLY ASN ALA PRO SER CYS LYS GLU GLU SEQRES 19 B 368 VAL THR SER LEU MET ASN SER VAL HIS LYS VAL ASN GLN SEQRES 20 B 368 GLN ILE GLN PRO LEU LEU ALA LEU ASN PRO VAL ASN GLU SEQRES 21 B 368 TRP TYR SER ILE GLY GLY ILE SER ASN LEU ALA SER SER SEQRES 22 B 368 GLN LEU PHE HIS PHE GLU ASN SER GLU LEU THR ASN GLN SEQRES 23 B 368 SER LEU LEU GLN GLN GLY ASP ASN GLN ILE CYS HIS GLN SEQRES 24 B 368 GLN TRP ASP ILE LEU ASN GLY GLN TYR PRO ASP ASP GLU SEQRES 25 B 368 TYR LEU TYR GLN TYR CYS LEU LEU SER SER TYR TYR TYR SEQRES 26 B 368 ALA LEU MET VAL ASP GLY TYR GLY ILE ASN PRO ASN GLN SEQRES 27 B 368 THR ILE HIS TYR ILE PRO PRO GLU GLN ASN LEU ASP TRP SEQRES 28 B 368 THR ILE GLY VAL VAL LEU HIS ARG ALA LEU GLU HIS HIS SEQRES 29 B 368 HIS HIS HIS HIS HET SO4 A1395 5 HET GOL A1396 12 HET SO4 A1397 5 HET SO4 B1396 5 HET SO4 B1397 10 HETNAM SO4 SULFATE ION HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 3 SO4 4(O4 S 2-) FORMUL 4 GOL C3 H8 O3 FORMUL 8 HOH *648(H2 O) HELIX 1 1 ASN A 37 LYS A 41 5 5 HELIX 2 2 GLY A 84 ILE A 88 5 5 HELIX 3 3 ASN A 91 ALA A 104 1 14 HELIX 4 4 THR A 118 LEU A 123 1 6 HELIX 5 5 PRO A 125 GLN A 142 1 18 HELIX 6 6 THR A 155 ASP A 172 1 18 HELIX 7 7 SER A 205 HIS A 207 5 3 HELIX 8 8 GLY A 230 HIS A 236 1 7 HELIX 9 9 SER A 241 PHE A 245 5 5 HELIX 10 10 ASN A 260 SER A 274 1 15 HELIX 11 11 LYS A 277 ASN A 289 1 13 HELIX 12 12 GLY A 299 SER A 305 1 7 HELIX 13 13 THR A 317 ILE A 329 1 13 HELIX 14 14 GLN A 333 TYR A 341 1 9 HELIX 15 15 TYR A 346 TYR A 348 5 3 HELIX 16 16 GLN A 349 VAL A 362 1 14 HELIX 17 17 PRO A 377 ASN A 381 5 5 HELIX 18 18 TRP A 384 ARG A 392 1 9 HELIX 19 19 ASN B 37 LYS B 41 5 5 HELIX 20 20 GLY B 84 ILE B 88 5 5 HELIX 21 21 ASN B 91 ALA B 104 1 14 HELIX 22 22 THR B 118 LEU B 123 1 6 HELIX 23 23 PRO B 125 GLN B 142 1 18 HELIX 24 24 THR B 155 ASP B 172 1 18 HELIX 25 25 SER B 205 HIS B 207 5 3 HELIX 26 26 GLY B 230 HIS B 236 1 7 HELIX 27 27 SER B 241 PHE B 245 5 5 HELIX 28 28 ASN B 260 SER B 274 1 15 HELIX 29 29 LYS B 277 ASN B 289 1 13 HELIX 30 30 GLY B 299 SER B 305 1 7 HELIX 31 31 ASN B 318 ILE B 329 1 12 HELIX 32 32 GLN B 333 TYR B 341 1 9 HELIX 33 33 TYR B 346 TYR B 348 5 3 HELIX 34 34 GLN B 349 VAL B 362 1 14 HELIX 35 35 PRO B 377 ASN B 381 5 5 HELIX 36 36 THR B 385 HIS B 391 1 7 SHEET 1 AA 5 PRO A 70 ILE A 81 0 SHEET 2 AA 5 SER A 55 THR A 64 -1 O SER A 55 N ILE A 81 SHEET 3 AA 5 SER A 43 ALA A 50 -1 O SER A 43 N TYR A 62 SHEET 4 AA 5 PRO A 112 ALA A 117 1 O PRO A 112 N ALA A 46 SHEET 5 AA 5 GLN A 147 THR A 153 1 O GLN A 147 N VAL A 113 SHEET 1 AB 7 GLN A 209 ILE A 214 0 SHEET 2 AB 7 GLN A 217 LEU A 227 -1 O GLN A 217 N ILE A 214 SHEET 3 AB 7 SER A 191 PRO A 197 -1 O VAL A 192 N PHE A 226 SHEET 4 AB 7 VAL A 182 MET A 187 -1 O VAL A 184 N VAL A 195 SHEET 5 AB 7 GLU A 293 GLY A 298 1 O GLU A 293 N GLY A 183 SHEET 6 AB 7 ILE A 373 TYR A 375 1 O HIS A 374 N SER A 296 SHEET 7 AB 7 GLU A 315 LEU A 316 -1 O LEU A 316 N ILE A 373 SHEET 1 BA 5 PRO B 70 ILE B 81 0 SHEET 2 BA 5 SER B 55 THR B 64 -1 O SER B 55 N ILE B 81 SHEET 3 BA 5 SER B 43 ALA B 50 -1 O SER B 43 N TYR B 62 SHEET 4 BA 5 ILE B 111 ALA B 117 1 O PRO B 112 N ALA B 46 SHEET 5 BA 5 TRP B 146 THR B 153 1 O GLN B 147 N VAL B 113 SHEET 1 BB 7 GLN B 209 ILE B 214 0 SHEET 2 BB 7 GLN B 217 PHE B 226 -1 O GLN B 217 N ILE B 214 SHEET 3 BB 7 VAL B 192 PRO B 197 -1 O VAL B 192 N PHE B 226 SHEET 4 BB 7 VAL B 182 MET B 187 -1 O VAL B 184 N VAL B 195 SHEET 5 BB 7 GLU B 293 GLY B 298 1 O GLU B 293 N GLY B 183 SHEET 6 BB 7 THR B 372 TYR B 375 1 O THR B 372 N TRP B 294 SHEET 7 BB 7 GLU B 315 THR B 317 -1 O LEU B 316 N ILE B 373 SSBOND 1 CYS A 39 CYS A 44 1555 1555 2.02 SSBOND 2 CYS A 244 CYS A 264 1555 1555 2.10 SSBOND 3 CYS A 330 CYS A 351 1555 1555 2.08 SSBOND 4 CYS B 39 CYS B 44 1555 1555 2.05 SSBOND 5 CYS B 244 CYS B 264 1555 1555 2.08 SSBOND 6 CYS B 330 CYS B 351 1555 1555 2.09 CISPEP 1 LYS A 82 PRO A 83 0 -2.01 CISPEP 2 LYS B 82 PRO B 83 0 -7.40 SITE 1 AC1 12 GLY A 51 SER A 52 THR A 118 ALA A 119 SITE 2 AC1 12 GLY A 188 GLY A 189 ALA A 190 SER A 191 SITE 3 AC1 12 HOH A2008 HOH A2016 HOH A2092 HOH A2363 SITE 1 AC2 9 LEU A 239 ASN A 240 HOH A2212 HOH A2221 SITE 2 AC2 9 LEU B 227 GLY B 228 HIS B 276 HOH B2155 SITE 3 AC2 9 HOH B2197 SITE 1 AC3 8 LEU A 308 GLN A 328 GLN A 332 LEU A 337 SITE 2 AC3 8 GLN A 340 TYR A 341 HOH A2329 HOH A2364 SITE 1 AC4 14 SER B 52 THR B 118 ALA B 119 GLU B 159 SITE 2 AC4 14 GLY B 188 GLY B 189 ALA B 190 SER B 191 SITE 3 AC4 14 HOH B2009 HOH B2016 HOH B2017 HOH B2081 SITE 4 AC4 14 HOH B2120 HOH B2121 SITE 1 AC5 9 PHE A 226 LEU A 227 HIS A 276 HOH A2199 SITE 2 AC5 9 HOH A2200 HOH A2267 HOH A2269 HOH A2365 SITE 3 AC5 9 ASN B 240 CRYST1 62.504 86.198 72.215 90.00 107.14 90.00 P 1 21 1 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 0.015999 0.000000 0.004934 0.00000 SCALE2 0.000000 0.011601 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014491 0.00000 MTRIX1 1 0.426000 0.089000 -0.900000 57.25200 1 MTRIX2 1 0.074000 -0.995000 -0.063000 2.98700 1 MTRIX3 1 -0.902000 -0.039000 -0.431000 91.53400 1