HEADER HYDROLASE 03-JUN-13 4BR4 TITLE LEGIONELLA PNEUMOPHILA NTPDASE1 CRYSTAL FORM I, OPEN, APO COMPND MOL_ID: 1; COMPND 2 MOLECULE: ECTONUCLEOSIDE TRIPHOSPHATE DIPHOSPHOHYDROLASE I; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 37-393; 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 5 16-OCT-24 4BR4 1 REMARK LINK REVDAT 4 23-AUG-17 4BR4 1 REMARK REVDAT 3 25-DEC-13 4BR4 1 KEYWDS REVDAT 2 28-AUG-13 4BR4 1 JRNL REVDAT 1 17-JUL-13 4BR4 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. 1.45 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) : 1.45 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 27.88 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 82021 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) : 0.146 REMARK 3 R VALUE (WORKING SET) : 0.145 REMARK 3 FREE R VALUE : 0.183 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 1.500 REMARK 3 FREE R VALUE TEST SET COUNT : 1211 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) : 1.45 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.49 REMARK 3 REFLECTION IN BIN (WORKING SET) : 6009 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.1800 REMARK 3 BIN FREE R VALUE SET COUNT : 79 REMARK 3 BIN FREE R VALUE : 0.2480 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2823 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 5 REMARK 3 SOLVENT ATOMS : 382 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 23.70 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.63000 REMARK 3 B22 (A**2) : 0.63000 REMARK 3 B33 (A**2) : -2.05000 REMARK 3 B12 (A**2) : 0.63000 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): 0.053 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.053 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.033 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.893 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.969 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.956 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2965 ; 0.022 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4063 ; 2.001 ; 1.937 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 375 ; 6.151 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 150 ;42.713 ;25.867 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 473 ;14.038 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 5 ;19.966 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 438 ; 0.138 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2327 ; 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): 2965 ; 7.358 ; 3.000 REMARK 3 SPHERICITY; FREE ATOMS (A**2): 115 ;37.189 ; 5.000 REMARK 3 SPHERICITY; BONDED ATOMS (A**2): 3148 ;20.198 ; 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 4BR4 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_1290057130. 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 : 14.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9181 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 83235 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.450 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 (%) : 100.0 REMARK 200 DATA REDUNDANCY : 6.200 REMARK 200 R MERGE (I) : 0.05000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 17.8000 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 (%): 56.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.80 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 30% PEP 629 (PENTAERYTHRITOL REMARK 280 PROPOXYLATE 17/8 PO/OH), 100MM NAHEPES PH 7.3, 50MM MGCL2 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 3 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z REMARK 290 6555 -X,-X+Y,-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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 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: 3720 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 28630 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -62.5 KCAL/MOL 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 350 BIOMT1 2 -0.500000 0.866025 0.000000 0.00000 REMARK 350 BIOMT2 2 0.866025 0.500000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 75.40400 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 MG MG A1396 LIES ON A SPECIAL POSITION. REMARK 375 MG MG A1397 LIES ON A SPECIAL POSITION. REMARK 375 HOH A2002 LIES ON A SPECIAL POSITION. REMARK 375 HOH A2217 LIES ON A SPECIAL POSITION. REMARK 375 HOH A2232 LIES ON A SPECIAL POSITION. REMARK 375 HOH A2233 LIES ON A SPECIAL POSITION. 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 29 REMARK 465 ASP A 30 REMARK 465 HIS A 31 REMARK 465 HIS A 32 REMARK 465 HIS A 33 REMARK 465 HIS A 34 REMARK 465 HIS A 35 REMARK 465 HIS A 36 REMARK 465 ASN A 37 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 ASN A 179 CB CG OD1 ND2 REMARK 470 LYS A 180 CG CD CE NZ REMARK 470 LYS A 206 CG CD CE NZ REMARK 470 GLU A 379 CB CG CD OE1 OE2 REMARK 470 ASN A 381 CG OD1 ND2 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 O SER A 144 O HOH A 2102 1.98 REMARK 500 O HOH A 2205 O HOH A 2206 2.08 REMARK 500 O HOH A 2277 O HOH A 2278 2.12 REMARK 500 O HOH A 2206 O HOH A 2207 2.13 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 GLU A 293 CD GLU A 293 OE2 -0.066 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ARG A 122 NE - CZ - NH2 ANGL. DEV. = -4.1 DEGREES REMARK 500 PRO A 125 C - N - CA ANGL. DEV. = -9.8 DEGREES REMARK 500 ASP A 248 CB - CG - OD1 ANGL. DEV. = 7.0 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 ASN A 110 60.70 68.96 REMARK 500 THR A 118 -141.21 -116.90 REMARK 500 ILE A 329 -56.72 -123.64 REMARK 500 GLU A 379 36.13 -73.47 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 ARG A 122 0.07 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A2058 DISTANCE = 6.32 ANGSTROMS REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A1396 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A2233 O REMARK 620 2 HOH A2233 O 0.1 REMARK 620 3 HOH A2235 O 87.5 87.6 REMARK 620 4 HOH A2235 O 87.6 87.5 175.1 REMARK 620 5 HOH A2381 O 88.0 88.0 91.6 88.2 REMARK 620 6 HOH A2381 O 88.0 88.0 88.2 91.6 176.0 REMARK 620 7 HOH A2382 O 174.6 174.7 92.9 92.0 86.6 97.4 REMARK 620 8 HOH A2382 O 174.6 174.5 92.0 92.9 97.4 86.6 10.8 REMARK 620 N 1 2 3 4 5 6 7 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A1397 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A2054 O REMARK 620 2 HOH A2054 O 175.8 REMARK 620 3 HOH A2217 O 87.9 88.0 REMARK 620 4 HOH A2217 O 87.9 87.9 0.1 REMARK 620 5 HOH A2378 O 87.3 93.3 94.8 94.7 REMARK 620 6 HOH A2378 O 93.0 87.1 94.5 94.6 170.7 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A1398 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A2037 O REMARK 620 2 HOH A2040 O 82.8 REMARK 620 3 HOH A2041 O 98.4 91.1 REMARK 620 4 HOH A2055 O 174.3 91.5 81.8 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 1394 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 1396 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 1397 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 1398 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 1395 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: 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 4BR4 A 37 393 UNP Q5ZUA2 Q5ZUA2_LEGPH 37 393 SEQADV 4BR4 MET A 29 UNP Q5ZUA2 EXPRESSION TAG SEQADV 4BR4 ASP A 30 UNP Q5ZUA2 EXPRESSION TAG SEQADV 4BR4 HIS A 31 UNP Q5ZUA2 EXPRESSION TAG SEQADV 4BR4 HIS A 32 UNP Q5ZUA2 EXPRESSION TAG SEQADV 4BR4 HIS A 33 UNP Q5ZUA2 EXPRESSION TAG SEQADV 4BR4 HIS A 34 UNP Q5ZUA2 EXPRESSION TAG SEQADV 4BR4 HIS A 35 UNP Q5ZUA2 EXPRESSION TAG SEQADV 4BR4 HIS A 36 UNP Q5ZUA2 EXPRESSION TAG SEQADV 4BR4 ASP A 137 UNP Q5ZUA2 GLU 137 CONFLICT SEQADV 4BR4 VAL A 149 UNP Q5ZUA2 ALA 149 CONFLICT SEQRES 1 A 365 MET ASP HIS HIS HIS HIS HIS HIS ASN PRO CYS GLU LYS SEQRES 2 A 365 HIS SER CYS ILE ALA VAL ILE ASP ALA GLY SER THR GLY SEQRES 3 A 365 SER ARG LEU HIS ILE TYR SER TYR ASP THR ASP ASP THR SEQRES 4 A 365 ASN THR PRO ILE HIS ILE GLU GLU ILE TRP ASN LYS LYS SEQRES 5 A 365 ILE LYS PRO GLY PHE ALA SER ILE GLN PRO ASN SER VAL SEQRES 6 A 365 THR ILE ASP ALA TYR LEU THR MET LEU LEU ALA ASP ALA SEQRES 7 A 365 PRO ILE HIS ASN ILE PRO VAL TYR PHE TYR ALA THR ALA SEQRES 8 A 365 GLY MET ARG LEU LEU PRO GLN SER GLN GLN LYS LYS TYR SEQRES 9 A 365 TYR ASP GLU LEU ASP TYR TRP PHE ARG GLN GLN SER GLN SEQRES 10 A 365 TRP GLN LEU VAL GLU ALA LYS THR ILE THR GLY ASN ASP SEQRES 11 A 365 GLU ALA LEU PHE ASP TRP LEU ALA VAL ASN TYR LYS LEU SEQRES 12 A 365 ASP THR LEU LYS SER VAL GLN ASN LYS SER VAL GLY VAL SEQRES 13 A 365 MET ASP MET GLY GLY ALA SER VAL GLN ILE VAL PHE PRO SEQRES 14 A 365 MET PRO LYS ASN ALA GLU ILE SER LYS HIS ASN GLN VAL SEQRES 15 A 365 GLU LEU ASN ILE TYR GLY GLN ASN ILE ASN LEU TYR VAL SEQRES 16 A 365 HIS SER PHE LEU GLY LEU GLY GLN THR GLU MET SER HIS SEQRES 17 A 365 GLN PHE LEU ASN SER PRO SER CYS PHE ALA ASN ASP TYR SEQRES 18 A 365 PRO LEU PRO ASP GLY GLU SER GLY GLN GLY ASN ALA PRO SEQRES 19 A 365 SER CYS LYS GLU GLU VAL THR SER LEU MET ASN SER VAL SEQRES 20 A 365 HIS LYS VAL ASN GLN GLN ILE GLN PRO LEU LEU ALA LEU SEQRES 21 A 365 ASN PRO VAL ASN GLU TRP TYR SER ILE GLY GLY ILE SER SEQRES 22 A 365 ASN LEU ALA SER SER GLN LEU PHE HIS PHE GLU ASN SER SEQRES 23 A 365 GLU LEU THR ASN GLN SER LEU LEU GLN GLN GLY ASP ASN SEQRES 24 A 365 GLN ILE CYS HIS GLN GLN TRP ASP ILE LEU ASN GLY GLN SEQRES 25 A 365 TYR PRO ASP ASP GLU TYR LEU TYR GLN TYR CYS LEU LEU SEQRES 26 A 365 SER SER TYR TYR TYR ALA LEU MET VAL ASP GLY TYR GLY SEQRES 27 A 365 ILE ASN PRO ASN GLN THR ILE HIS TYR ILE PRO PRO GLU SEQRES 28 A 365 GLN ASN LEU ASP TRP THR ILE GLY VAL VAL LEU HIS ARG SEQRES 29 A 365 ALA HET CL A1394 1 HET CL A1395 1 HET MG A1396 1 HET MG A1397 1 HET MG A1398 1 HETNAM CL CHLORIDE ION HETNAM MG MAGNESIUM ION FORMUL 2 CL 2(CL 1-) FORMUL 4 MG 3(MG 2+) FORMUL 7 HOH *382(H2 O) HELIX 1 1 GLY A 84 ILE A 88 5 5 HELIX 2 2 ASN A 91 ALA A 104 1 14 HELIX 3 3 THR A 118 LEU A 123 1 6 HELIX 4 4 PRO A 125 GLN A 142 1 18 HELIX 5 5 THR A 155 ASP A 172 1 18 HELIX 6 6 SER A 205 HIS A 207 5 3 HELIX 7 7 GLY A 230 HIS A 236 1 7 HELIX 8 8 SER A 241 PHE A 245 5 5 HELIX 9 9 ASN A 260 VAL A 275 1 16 HELIX 10 10 LYS A 277 ASN A 289 1 13 HELIX 11 11 GLY A 299 SER A 305 1 7 HELIX 12 12 ASN A 318 ILE A 329 1 12 HELIX 13 13 GLN A 333 TYR A 341 1 9 HELIX 14 14 TYR A 346 TYR A 348 5 3 HELIX 15 15 GLN A 349 VAL A 362 1 14 HELIX 16 16 PRO A 377 ASN A 381 5 5 HELIX 17 17 TRP A 384 ALA A 393 1 10 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 ILE A 111 ALA A 117 1 O PRO A 112 N ALA A 46 SHEET 5 AA 5 TRP A 146 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 THR A 372 TYR A 375 1 O THR A 372 N TRP A 294 SHEET 7 AB 7 GLU A 315 THR A 317 -1 O LEU A 316 N ILE A 373 SSBOND 1 CYS A 39 CYS A 44 1555 1555 1.99 SSBOND 2 CYS A 244 CYS A 264 1555 1555 2.12 SSBOND 3 CYS A 330 CYS A 351 1555 1555 2.13 LINK MG MG A1396 O HOH A2233 1555 1555 2.05 LINK MG MG A1396 O HOH A2233 1555 4556 2.05 LINK MG MG A1396 O HOH A2235 1555 1555 1.97 LINK MG MG A1396 O HOH A2235 1555 4556 1.97 LINK MG MG A1396 O HOH A2381 1555 1555 2.12 LINK MG MG A1396 O HOH A2381 1555 4556 2.12 LINK MG MG A1396 O HOH A2382 1555 1555 2.08 LINK MG MG A1396 O HOH A2382 1555 4556 2.08 LINK MG MG A1397 O HOH A2054 1555 4555 1.91 LINK MG MG A1397 O HOH A2054 1555 1555 1.91 LINK MG MG A1397 O HOH A2217 1555 1555 2.51 LINK MG MG A1397 O HOH A2217 1555 4555 2.51 LINK MG MG A1397 O HOH A2378 1555 1555 2.37 LINK MG MG A1397 O HOH A2378 1555 4555 2.37 LINK MG MG A1398 O HOH A2037 1555 1555 2.12 LINK MG MG A1398 O HOH A2040 1555 1555 1.97 LINK MG MG A1398 O HOH A2041 1555 1555 2.18 LINK MG MG A1398 O HOH A2055 1555 1555 2.24 CISPEP 1 LYS A 82 PRO A 83 0 -2.24 SITE 1 AC1 6 ARG A 122 GLY A 156 ASN A 240 ASP A 253 SITE 2 AC1 6 HOH A2110 HOH A2164 SITE 1 AC2 4 HOH A2233 HOH A2235 HOH A2381 HOH A2382 SITE 1 AC3 3 HOH A2054 HOH A2217 HOH A2378 SITE 1 AC4 4 HOH A2037 HOH A2040 HOH A2041 HOH A2055 SITE 1 AC5 4 ASN A 327 GLN A 328 HOH A2317 HOH A2337 CRYST1 103.875 103.875 75.404 90.00 90.00 120.00 P 3 2 1 6 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 0.009627 0.005558 0.000000 0.00000 SCALE2 0.000000 0.011116 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013262 0.00000