PDB Short entry for 3QUT HEADER HYDROLASE 24-FEB-11 3QUT TITLE CRYSTAL STRUCTURE OF PYROPHOSPHATASE FROM BACTEROIDES TITLE 2 THETAIOTAOMICRON, ASP13ASN MUTANT, AN OPEN CAP CONFORMATION COMPND MOL_ID: 1; COMPND 2 MOLECULE: INORGANIC PYROPHOSPHATASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: PUTATIVE BETA-PHOSPHOGLUCOMUTASE; COMPND 5 EC: 3.6.1.1; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BACTEROIDES THETAIOTAOMICRON; SOURCE 3 ORGANISM_TAXID: 818; SOURCE 4 GENE: BT_2127; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS HYDROLASE, PYROPHOSPHATASE, MAGNESIUM BINDING SITE, NEW YORK SGX KEYWDS 2 RESEARCH CENTER FOR STRUCTURAL GENOMICS, NYSGX ENZYME FUNCTION KEYWDS 3 INITIATIVE, EFI, PSI-2, PROTEIN STRUCTURE INITIATIVE, NYSGXRC EXPDTA X-RAY DIFFRACTION AUTHOR Y.PATSKOVSKY,H.HUANG,R.TORO,J.A.GERLT,S.K.BURLEY,D.DUNAWAY-MARIANO, AUTHOR 2 S.C.ALMO,NEW YORK SGX RESEARCH CENTER FOR STRUCTURAL GENOMICS AUTHOR 3 (NYSGXRC),ENZYME FUNCTION INITIATIVE (EFI) REVDAT 5 13-SEP-23 3QUT 1 REMARK REVDAT 4 10-FEB-21 3QUT 1 AUTHOR REMARK SEQADV LINK REVDAT 3 24-JAN-18 3QUT 1 AUTHOR REVDAT 2 16-NOV-11 3QUT 1 JRNL VERSN REVDAT 1 13-APR-11 3QUT 0 JRNL AUTH H.HUANG,Y.PATSKOVSKY,R.TORO,J.D.FARELLI,C.PANDYA,S.C.ALMO, JRNL AUTH 2 K.N.ALLEN,D.DUNAWAY-MARIANO JRNL TITL DIVERGENCE OF STRUCTURE AND FUNCTION IN THE HALOACID JRNL TITL 2 DEHALOGENASE ENZYME SUPERFAMILY: BACTEROIDES JRNL TITL 3 THETAIOTAOMICRON BT2127 IS AN INORGANIC PYROPHOSPHATASE. JRNL REF BIOCHEMISTRY V. 50 8937 2011 JRNL REFN ISSN 0006-2960 JRNL PMID 21894910 JRNL DOI 10.1021/BI201181Q REMARK 2 REMARK 2 RESOLUTION. 1.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0109 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) : 1.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 49.63 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 35951 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) : 0.145 REMARK 3 R VALUE (WORKING SET) : 0.145 REMARK 3 FREE R VALUE : 0.172 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 3.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1152 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) : 1.50 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.54 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2629 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.96 REMARK 3 BIN R VALUE (WORKING SET) : 0.2050 REMARK 3 BIN FREE R VALUE SET COUNT : 74 REMARK 3 BIN FREE R VALUE : 0.2890 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1752 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 12 REMARK 3 SOLVENT ATOMS : 243 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 18.42 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 25.06 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.32000 REMARK 3 B22 (A**2) : 0.42000 REMARK 3 B33 (A**2) : -0.74000 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): 0.075 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.062 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.036 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.095 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.975 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.969 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1857 ; 0.011 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2522 ; 1.387 ; 1.973 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 242 ; 5.717 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 80 ;37.779 ;24.625 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 336 ;14.948 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 8 ;22.207 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 277 ; 0.091 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1403 ; 0.007 ; 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): 1144 ; 3.908 ; 2.000 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1847 ; 5.525 ; 3.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 713 ; 7.270 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 666 ; 9.836 ; 5.000 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): 1857 ; 2.546 ; 1.000 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 : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : BABINET MODEL WITH 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: NULL REMARK 4 REMARK 4 3QUT COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 03-MAR-11. REMARK 100 THE DEPOSITION ID IS D_1000064130. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 23-JAN-10 REMARK 200 TEMPERATURE (KELVIN) : 90 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X29A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9791 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 37187 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.500 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -5.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 8.000 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.06700 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 7.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.53 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 7.50 REMARK 200 R MERGE FOR SHELL (I) : 0.60000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MR REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 3QU2 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 38.42 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.00 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.15M MALIC ACID, PH 7, 20% PEG3350, REMARK 280 5MM MAGNESIUM CHLORIDE, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 294K, PH 7.0 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 22.73750 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 38.08400 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 32.70250 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 38.08400 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 22.73750 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 32.70250 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 GLY A -18 REMARK 465 SER A -17 REMARK 465 SER A -16 REMARK 465 HIS A -15 REMARK 465 HIS A -14 REMARK 465 HIS A -13 REMARK 465 HIS A -12 REMARK 465 HIS A -11 REMARK 465 HIS A -10 REMARK 465 SER A -9 REMARK 465 SER A -8 REMARK 465 GLY A -7 REMARK 465 LEU A -6 REMARK 465 VAL A -5 REMARK 465 PRO A -4 REMARK 465 ARG A -3 REMARK 465 GLY A -2 REMARK 465 SER A -1 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 LEU A 120 CG CD1 CD2 REMARK 470 GLU A 122 CG CD OE1 OE2 REMARK 470 MET A 223 CE 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 ARG A 91 CZ ARG A 91 NH1 -0.081 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 MET A 12 -70.50 -92.41 REMARK 500 VAL A 15 -60.53 -126.51 REMARK 500 GLN A 117 93.28 -67.51 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 225 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 11 OD2 REMARK 620 2 ASN A 13 O 87.4 REMARK 620 3 GLU A 47 OE2 170.0 94.6 REMARK 620 4 ASN A 172 OD1 85.3 87.7 104.5 REMARK 620 5 MLT A 227 O3 86.6 94.4 83.4 171.6 REMARK 620 6 HOH A 232 O 84.4 171.4 94.0 89.1 87.7 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 226 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASN A 191 O REMARK 620 2 PRO A 210 O 80.6 REMARK 620 3 HOH A 254 O 85.1 148.0 REMARK 620 4 HOH A 370 O 106.9 112.0 99.5 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 MG A 225 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 226 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MLT A 227 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 228 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: NYSGXRC-22199A RELATED DB: TARGETDB REMARK 900 RELATED ID: 3QU2 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF PYROPHOSPHATASE FROM BACTEROIDES REMARK 900 THETAIOTAOMICRON, A CLOSED CAP CONFORMATION, WILD-TYPE PROTEIN REMARK 900 RELATED ID: 3QU4 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF PYROPHOSPHATASE FROM BACTEROIDES REMARK 900 THETAIOTAOMICRON, ASP13ALA MUTANT REMARK 900 RELATED ID: 3QU5 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF PYROPHOSPHATASE FROM BACTEROIDES REMARK 900 THETAIOTAOMICRON, ASP11ASN MUTANT REMARK 900 RELATED ID: 3QU7 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF PYROPHOSPHATASE FROM BACTEROIDES REMARK 900 THETAIOTAOMICRON, ASP13ASN MUTANT COMPLEXED WITH CALCIUM AND REMARK 900 PHOSPHATE REMARK 900 RELATED ID: 3QU9 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF PYROPHOSPHATASE FROM BACTEROIDES REMARK 900 THETAIOTAOMICRON, ASP13ASN MUTANT COMPLEXED WITH MAGNESIUM AND REMARK 900 TARTRATE REMARK 900 RELATED ID: 3QUB RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF PYROPHOSPHATASE FROM BACTEROIDES REMARK 900 THETAIOTAOMICRON, GLU47ALA MUTANT COMPLEXED WITH SULFATE REMARK 900 RELATED ID: 3QUC RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF PYROPHOSPHATASE FROM BACTEROIDES REMARK 900 THETAIOTAOMICRON, GLU47ASN MUTANT COMPLEXED WITH SULFATE REMARK 900 RELATED ID: 3QUQ RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF PYROPHOSPHATASE FROM BACTEROIDES REMARK 900 THETAIOTAOMICRON, AN OPEN CAP CONFORMATION, WILD-TYPE PROTEIN REMARK 900 RELATED ID: 3QYP RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF PYROPHOSPHATASE FROM BACTEROIDES REMARK 900 THETAIOTAOMICRON, GLU47ASN MUTANT COMPLEXED WITH CALCIUM AND REMARK 900 PHOSPHATE REMARK 900 RELATED ID: 3QX7 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF PYROPHOSPHATASE FROM BACTEROIDES REMARK 900 THETAIOTAOMICRON COMPLEXED WITH PHOSPHATE, A CLOSED CAP REMARK 900 CONFORMATION, WILD-TYPE PROTEIN REMARK 900 RELATED ID: 3QXG RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF PYROPHOSPHATASE FROM BACTEROIDES REMARK 900 THETAIOTAOMICRON COMPLEXED WITH CALCIUM, A CLOSED CAP CONFORMATION, REMARK 900 WILD-TYPE PROTEIN REMARK 900 RELATED ID: 3R9K RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF PYROPHOSPHATASE FROM BACTEROIDES REMARK 900 THETAIOTAOMICRON, GLU47ASP MUTANT COMPLEXED WITH SULFATE, A CLOSED REMARK 900 CAP CONFORMATION DBREF 3QUT A 1 224 UNP Q8A5V9 Q8A5V9_BACTN 1 224 SEQADV 3QUT GLY A -18 UNP Q8A5V9 EXPRESSION TAG SEQADV 3QUT SER A -17 UNP Q8A5V9 EXPRESSION TAG SEQADV 3QUT SER A -16 UNP Q8A5V9 EXPRESSION TAG SEQADV 3QUT HIS A -15 UNP Q8A5V9 EXPRESSION TAG SEQADV 3QUT HIS A -14 UNP Q8A5V9 EXPRESSION TAG SEQADV 3QUT HIS A -13 UNP Q8A5V9 EXPRESSION TAG SEQADV 3QUT HIS A -12 UNP Q8A5V9 EXPRESSION TAG SEQADV 3QUT HIS A -11 UNP Q8A5V9 EXPRESSION TAG SEQADV 3QUT HIS A -10 UNP Q8A5V9 EXPRESSION TAG SEQADV 3QUT SER A -9 UNP Q8A5V9 EXPRESSION TAG SEQADV 3QUT SER A -8 UNP Q8A5V9 EXPRESSION TAG SEQADV 3QUT GLY A -7 UNP Q8A5V9 EXPRESSION TAG SEQADV 3QUT LEU A -6 UNP Q8A5V9 EXPRESSION TAG SEQADV 3QUT VAL A -5 UNP Q8A5V9 EXPRESSION TAG SEQADV 3QUT PRO A -4 UNP Q8A5V9 EXPRESSION TAG SEQADV 3QUT ARG A -3 UNP Q8A5V9 EXPRESSION TAG SEQADV 3QUT GLY A -2 UNP Q8A5V9 EXPRESSION TAG SEQADV 3QUT SER A -1 UNP Q8A5V9 EXPRESSION TAG SEQADV 3QUT HIS A 0 UNP Q8A5V9 EXPRESSION TAG SEQADV 3QUT ASN A 13 UNP Q8A5V9 ASP 13 ENGINEERED MUTATION SEQRES 1 A 243 GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY LEU SEQRES 2 A 243 VAL PRO ARG GLY SER HIS MET ARG LYS LYS LEU LYS ALA SEQRES 3 A 243 VAL LEU PHE ASP MET ASN GLY VAL LEU PHE ASN SER MET SEQRES 4 A 243 PRO TYR HIS SER GLU ALA TRP HIS GLN VAL MET LYS THR SEQRES 5 A 243 HIS GLY LEU ASP LEU SER ARG GLU GLU ALA TYR MET HIS SEQRES 6 A 243 GLU GLY ARG THR GLY ALA SER THR ILE ASN ILE VAL PHE SEQRES 7 A 243 GLN ARG GLU LEU GLY LYS GLU ALA THR GLN GLU GLU ILE SEQRES 8 A 243 GLU SER ILE TYR HIS GLU LYS SER ILE LEU PHE ASN SER SEQRES 9 A 243 TYR PRO GLU ALA GLU ARG MET PRO GLY ALA TRP GLU LEU SEQRES 10 A 243 LEU GLN LYS VAL LYS SER GLU GLY LEU THR PRO MET VAL SEQRES 11 A 243 VAL THR GLY SER GLY GLN LEU SER LEU LEU GLU ARG LEU SEQRES 12 A 243 GLU HIS ASN PHE PRO GLY MET PHE HIS LYS GLU LEU MET SEQRES 13 A 243 VAL THR ALA PHE ASP VAL LYS TYR GLY LYS PRO ASN PRO SEQRES 14 A 243 GLU PRO TYR LEU MET ALA LEU LYS LYS GLY GLY LEU LYS SEQRES 15 A 243 ALA ASP GLU ALA VAL VAL ILE GLU ASN ALA PRO LEU GLY SEQRES 16 A 243 VAL GLU ALA GLY HIS LYS ALA GLY ILE PHE THR ILE ALA SEQRES 17 A 243 VAL ASN THR GLY PRO LEU ASP GLY GLN VAL LEU LEU ASP SEQRES 18 A 243 ALA GLY ALA ASP LEU LEU PHE PRO SER MET GLN THR LEU SEQRES 19 A 243 CYS ASP SER TRP ASP THR ILE MET LEU HET MG A 225 1 HET MG A 226 1 HET MLT A 227 9 HET CL A 228 1 HETNAM MG MAGNESIUM ION HETNAM MLT D-MALATE HETNAM CL CHLORIDE ION HETSYN MLT (2R)-2-HYDROXYBUTANEDIOIC ACID; 2-HYDROXY-SUCCINIC ACID FORMUL 2 MG 2(MG 2+) FORMUL 4 MLT C4 H6 O5 FORMUL 5 CL CL 1- FORMUL 6 HOH *243(H2 O) HELIX 1 1 HIS A 0 LEU A 5 1 6 HELIX 2 2 SER A 19 HIS A 34 1 16 HELIX 3 3 SER A 39 HIS A 46 1 8 HELIX 4 4 THR A 50 GLY A 64 1 15 HELIX 5 5 THR A 68 TYR A 86 1 19 HELIX 6 6 GLY A 94 GLU A 105 1 12 HELIX 7 7 GLN A 117 GLU A 122 1 6 HELIX 8 8 GLU A 122 PHE A 128 1 7 HELIX 9 9 HIS A 133 GLU A 135 5 3 HELIX 10 10 THR A 139 VAL A 143 5 5 HELIX 11 11 PRO A 150 GLY A 161 1 12 HELIX 12 12 LYS A 163 ASP A 165 5 3 HELIX 13 13 ALA A 173 ALA A 183 1 11 HELIX 14 14 ASP A 196 ALA A 203 1 8 HELIX 15 15 SER A 211 LEU A 224 1 14 SHEET 1 A 6 MET A 137 VAL A 138 0 SHEET 2 A 6 THR A 108 VAL A 112 1 N VAL A 111 O VAL A 138 SHEET 3 A 6 ALA A 7 PHE A 10 1 N PHE A 10 O MET A 110 SHEET 4 A 6 ALA A 167 GLU A 171 1 O VAL A 168 N LEU A 9 SHEET 5 A 6 PHE A 186 VAL A 190 1 O ILE A 188 N VAL A 169 SHEET 6 A 6 LEU A 207 PHE A 209 1 O LEU A 207 N ALA A 189 LINK OD2 ASP A 11 MG MG A 225 1555 1555 2.03 LINK O ASN A 13 MG MG A 225 1555 1555 2.17 LINK OE2 GLU A 47 MG MG A 225 1555 1555 2.00 LINK OD1 ASN A 172 MG MG A 225 1555 1555 2.16 LINK O ASN A 191 MG MG A 226 1555 1555 2.34 LINK O PRO A 210 MG MG A 226 1555 1555 2.31 LINK MG MG A 225 O3 MLT A 227 1555 1555 2.12 LINK MG MG A 225 O HOH A 232 1555 1555 2.16 LINK MG MG A 226 O HOH A 254 1555 1555 2.33 LINK MG MG A 226 O HOH A 370 1555 1555 2.36 CISPEP 1 LYS A 147 PRO A 148 0 16.66 SITE 1 AC1 6 ASP A 11 ASN A 13 GLU A 47 ASN A 172 SITE 2 AC1 6 MLT A 227 HOH A 232 SITE 1 AC2 6 HIS A 126 PRO A 129 ASN A 191 PRO A 210 SITE 2 AC2 6 HOH A 254 HOH A 370 SITE 1 AC3 14 ASP A 11 MET A 12 ASN A 13 GLU A 47 SITE 2 AC3 14 GLY A 48 THR A 113 GLY A 114 SER A 115 SITE 3 AC3 14 LYS A 147 MG A 225 HOH A 232 HOH A 233 SITE 4 AC3 14 HOH A 259 HOH A 287 SITE 1 AC4 2 ARG A 40 HOH A 316 CRYST1 45.475 65.405 76.168 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 0.021990 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015289 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013129 0.00000