HEADER HYDROLASE 01-SEP-03 1QW7 TITLE STRUCTURE OF AN ENGINEERED ORGANOPHOSPHOROUS HYDROLASE WITH INCREASED TITLE 2 ACTIVITY TOWARD HYDROLYSIS OF PHOSPHOTHIOLATE BONDS COMPND MOL_ID: 1; COMPND 2 MOLECULE: PARATHION HYDROLASE; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: PHOSPHOTRIESTERASE, PTE; COMPND 5 EC: 3.1.8.1; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BREVUNDIMONAS DIMINUTA; SOURCE 3 ORGANISM_TAXID: 293; SOURCE 4 GENE: OPD; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS ORGANOPHOSPHOROUS HYDROLASE, PHOSPHOTRIESTERASE, VX, RVX, 4- KEYWDS 2 METHYLBENZYLPHOSPHONATE, MUTANT, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR A.D.MESECAR,J.K.GRIMSLEY,T.HOLTON,J.R.WILD REVDAT 7 15-NOV-23 1QW7 1 REMARK REVDAT 6 16-AUG-23 1QW7 1 REMARK REVDAT 5 27-OCT-21 1QW7 1 REMARK SEQADV LINK REVDAT 4 30-JUN-09 1QW7 1 JRNL REVDAT 3 23-JUN-09 1QW7 1 HET HETATM HETNAM SEQADV REVDAT 2 24-FEB-09 1QW7 1 VERSN REVDAT 1 30-NOV-04 1QW7 0 JRNL AUTH J.K.GRIMSLEY,B.CALAMINI,J.R.WILD,A.D.MESECAR JRNL TITL STRUCTURAL AND MUTATIONAL STUDIES OF ORGANOPHOSPHORUS JRNL TITL 2 HYDROLASE REVEAL A CRYPTIC AND FUNCTIONAL ALLOSTERIC-BINDING JRNL TITL 3 SITE. JRNL REF ARCH.BIOCHEM.BIOPHYS. V. 442 169 2005 JRNL REFN ISSN 0003-9861 JRNL PMID 16188223 JRNL DOI 10.1016/J.ABB.2005.08.012 REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.0 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 49.50 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 2312372.180 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 79.4 REMARK 3 NUMBER OF REFLECTIONS : 47941 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 SET) : 0.179 REMARK 3 FREE R VALUE : 0.230 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2407 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.005 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 10 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.90 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.97 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 43.60 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2477 REMARK 3 BIN R VALUE (WORKING SET) : 0.2990 REMARK 3 BIN FREE R VALUE : 0.3430 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.00 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 130 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.030 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5124 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 38 REMARK 3 SOLVENT ATOMS : 525 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 15.50 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 26.50 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 11.70000 REMARK 3 B22 (A**2) : 0.60000 REMARK 3 B33 (A**2) : -12.30000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 7.06000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.21 REMARK 3 ESD FROM SIGMAA (A) : 0.25 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.26 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.31 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.013 REMARK 3 BOND ANGLES (DEGREES) : 1.700 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 22.70 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.030 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 2.480 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 3.030 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 3.740 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 4.690 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.37 REMARK 3 BSOL : 54.69 REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : ION.PARAM REMARK 3 PARAMETER FILE 3 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 4 : EBP.PARAM REMARK 3 PARAMETER FILE 5 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : ION.TOP REMARK 3 TOPOLOGY FILE 3 : WATER.TOP REMARK 3 TOPOLOGY FILE 4 : EBP.TOP REMARK 3 TOPOLOGY FILE 5 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1QW7 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 04-SEP-03. REMARK 100 THE DEPOSITION ID IS D_1000020143. 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 : 9 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 5.0.2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.15 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 48009 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 49.500 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 79.4 REMARK 200 DATA REDUNDANCY : 7.300 REMARK 200 R MERGE (I) : 0.11500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.97 REMARK 200 COMPLETENESS FOR SHELL (%) : 43.6 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.24400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.200 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: CNS REMARK 200 STARTING MODEL: PDB ENTRY 1DPM REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.98 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.67 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 9% PEG 6000, 1% 4 REMARK 280 -METYLBENZYLPHOSPHONATE, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 293K, PH 9 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 63.35950 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 44.93950 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 63.35950 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 44.93950 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 300 REMARK: BIOLOGICAL UNIT IS A DIMER WHICH IS CONTAINED WITHIN THE REMARK 300 ASSYMETRIC UNIT AS CHAIN A AND CHAIN B 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: 4290 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 23410 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -73.0 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 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 HOH B 774 O HOH B 776 1.98 REMARK 500 OD1 ASP B 236 O HOH B 870 2.15 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 ALA A 203 N - CA - C ANGL. DEV. = -19.6 DEGREES REMARK 500 ALA B 203 N - CA - C ANGL. DEV. = -18.9 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 SER A 61 -143.43 -135.19 REMARK 500 THR A 128 -168.27 -116.37 REMARK 500 TRP A 131 -155.08 -94.43 REMARK 500 TRP A 131 -153.50 -94.43 REMARK 500 GLU A 159 -134.75 51.20 REMARK 500 SER B 61 -141.94 -135.63 REMARK 500 TRP B 131 -155.76 -95.80 REMARK 500 TRP B 131 -156.33 -95.80 REMARK 500 GLU B 159 -130.42 56.54 REMARK 500 THR B 173 69.74 -116.11 REMARK 500 THR B 173 71.07 -116.41 REMARK 500 TYR B 292 44.95 -104.81 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 NA A 605 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASN A 38 OD1 REMARK 620 2 ILE A 154 O 92.5 REMARK 620 3 HOH A 913 O 67.6 144.9 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CO A 602 CO REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 55 NE2 REMARK 620 2 HIS A 57 NE2 102.7 REMARK 620 3 KCX A 169 OQ2 86.7 94.3 REMARK 620 4 ASP A 301 OD2 82.0 90.7 168.4 REMARK 620 5 HOH A 802 O 102.0 153.2 76.7 103.1 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CO A 601 CO REMARK 620 N RES CSSEQI ATOM REMARK 620 1 KCX A 169 OQ1 REMARK 620 2 HIS A 201 ND1 98.1 REMARK 620 3 HIS A 230 NE2 103.5 85.7 REMARK 620 4 HOH A 802 O 100.8 160.5 94.4 REMARK 620 5 HOH A 826 O 113.7 97.2 141.8 70.8 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA B 606 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASN B 38 OD1 REMARK 620 2 ILE B 154 O 93.6 REMARK 620 3 HOH B 802 O 65.2 143.7 REMARK 620 4 HOH B 830 O 124.2 111.2 105.1 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CO B 603 CO REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 55 NE2 REMARK 620 2 HIS B 57 NE2 104.7 REMARK 620 3 KCX B 169 OQ2 87.7 100.4 REMARK 620 4 ASP B 301 OD2 81.2 84.7 168.7 REMARK 620 5 HOH B 774 O 101.8 152.8 74.4 105.6 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CO B 604 CO REMARK 620 N RES CSSEQI ATOM REMARK 620 1 KCX B 169 OQ1 REMARK 620 2 HIS B 201 ND1 92.3 REMARK 620 3 HIS B 230 NE2 103.1 88.2 REMARK 620 4 HOH B 774 O 115.4 151.8 90.4 REMARK 620 5 HOH B 776 O 114.4 95.9 142.0 68.7 REMARK 620 N 1 2 3 4 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CO A 601 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CO A 602 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CO B 603 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CO B 604 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 605 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA B 606 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EBP B 701 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EBP A 702 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1DPM RELATED DB: PDB REMARK 900 THREE-DIMENSIONAL STRUCTURE OF THE ZINC-CONTAINING REMARK 900 PHOSPHOTRIESTERASE WITH BOUND SUBSTRATE ANALOG DIETHYL 4- REMARK 900 METHYLBENZYLPHOSPHONATE DBREF 1QW7 A 30 365 UNP P0A434 OPD_BREDI 30 365 DBREF 1QW7 B 30 365 UNP P0A434 OPD_BREDI 30 365 SEQADV 1QW7 ARG A 254 UNP P0A434 HIS 254 ENGINEERED MUTATION SEQADV 1QW7 ARG B 254 UNP P0A434 HIS 254 ENGINEERED MUTATION SEQRES 1 A 336 SER ILE GLY THR GLY ASP ARG ILE ASN THR VAL ARG GLY SEQRES 2 A 336 PRO ILE THR ILE SER GLU ALA GLY PHE THR LEU THR HIS SEQRES 3 A 336 GLU HIS ILE CYS GLY SER SER ALA GLY PHE LEU ARG ALA SEQRES 4 A 336 TRP PRO GLU PHE PHE GLY SER ARG LYS ALA LEU ALA GLU SEQRES 5 A 336 LYS ALA VAL ARG GLY LEU ARG ARG ALA ARG ALA ALA GLY SEQRES 6 A 336 VAL ARG THR ILE VAL ASP VAL SER THR PHE ASP ILE GLY SEQRES 7 A 336 ARG ASP VAL SER LEU LEU ALA GLU VAL SER ARG ALA ALA SEQRES 8 A 336 ASP VAL HIS ILE VAL ALA ALA THR GLY LEU TRP PHE ASP SEQRES 9 A 336 PRO PRO LEU SER MET ARG LEU ARG SER VAL GLU GLU LEU SEQRES 10 A 336 THR GLN PHE PHE LEU ARG GLU ILE GLN TYR GLY ILE GLU SEQRES 11 A 336 ASP THR GLY ILE ARG ALA GLY ILE ILE KCX VAL ALA THR SEQRES 12 A 336 THR GLY LYS ALA THR PRO PHE GLN GLU LEU VAL LEU LYS SEQRES 13 A 336 ALA ALA ALA ARG ALA SER LEU ALA THR GLY VAL PRO VAL SEQRES 14 A 336 THR THR HIS THR ALA ALA SER GLN ARG ASP GLY GLU GLN SEQRES 15 A 336 GLN ALA ALA ILE PHE GLU SER GLU GLY LEU SER PRO SER SEQRES 16 A 336 ARG VAL CYS ILE GLY HIS SER ASP ASP THR ASP ASP LEU SEQRES 17 A 336 SER TYR LEU THR ALA LEU ALA ALA ARG GLY TYR LEU ILE SEQRES 18 A 336 GLY LEU ASP ARG ILE PRO HIS SER ALA ILE GLY LEU GLU SEQRES 19 A 336 ASP ASN ALA SER ALA SER ALA LEU LEU GLY ILE ARG SER SEQRES 20 A 336 TRP GLN THR ARG ALA LEU LEU ILE LYS ALA LEU ILE ASP SEQRES 21 A 336 GLN GLY TYR MET LYS GLN ILE LEU VAL SER ASN ASP TRP SEQRES 22 A 336 LEU PHE GLY PHE SER SER TYR VAL THR ASN ILE MET ASP SEQRES 23 A 336 VAL MET ASP ARG VAL ASN PRO ASP GLY MET ALA PHE ILE SEQRES 24 A 336 PRO LEU ARG VAL ILE PRO PHE LEU ARG GLU LYS GLY VAL SEQRES 25 A 336 PRO GLN GLU THR LEU ALA GLY ILE THR VAL THR ASN PRO SEQRES 26 A 336 ALA ARG PHE LEU SER PRO THR LEU ARG ALA SER SEQRES 1 B 336 SER ILE GLY THR GLY ASP ARG ILE ASN THR VAL ARG GLY SEQRES 2 B 336 PRO ILE THR ILE SER GLU ALA GLY PHE THR LEU THR HIS SEQRES 3 B 336 GLU HIS ILE CYS GLY SER SER ALA GLY PHE LEU ARG ALA SEQRES 4 B 336 TRP PRO GLU PHE PHE GLY SER ARG LYS ALA LEU ALA GLU SEQRES 5 B 336 LYS ALA VAL ARG GLY LEU ARG ARG ALA ARG ALA ALA GLY SEQRES 6 B 336 VAL ARG THR ILE VAL ASP VAL SER THR PHE ASP ILE GLY SEQRES 7 B 336 ARG ASP VAL SER LEU LEU ALA GLU VAL SER ARG ALA ALA SEQRES 8 B 336 ASP VAL HIS ILE VAL ALA ALA THR GLY LEU TRP PHE ASP SEQRES 9 B 336 PRO PRO LEU SER MET ARG LEU ARG SER VAL GLU GLU LEU SEQRES 10 B 336 THR GLN PHE PHE LEU ARG GLU ILE GLN TYR GLY ILE GLU SEQRES 11 B 336 ASP THR GLY ILE ARG ALA GLY ILE ILE KCX VAL ALA THR SEQRES 12 B 336 THR GLY LYS ALA THR PRO PHE GLN GLU LEU VAL LEU LYS SEQRES 13 B 336 ALA ALA ALA ARG ALA SER LEU ALA THR GLY VAL PRO VAL SEQRES 14 B 336 THR THR HIS THR ALA ALA SER GLN ARG ASP GLY GLU GLN SEQRES 15 B 336 GLN ALA ALA ILE PHE GLU SER GLU GLY LEU SER PRO SER SEQRES 16 B 336 ARG VAL CYS ILE GLY HIS SER ASP ASP THR ASP ASP LEU SEQRES 17 B 336 SER TYR LEU THR ALA LEU ALA ALA ARG GLY TYR LEU ILE SEQRES 18 B 336 GLY LEU ASP ARG ILE PRO HIS SER ALA ILE GLY LEU GLU SEQRES 19 B 336 ASP ASN ALA SER ALA SER ALA LEU LEU GLY ILE ARG SER SEQRES 20 B 336 TRP GLN THR ARG ALA LEU LEU ILE LYS ALA LEU ILE ASP SEQRES 21 B 336 GLN GLY TYR MET LYS GLN ILE LEU VAL SER ASN ASP TRP SEQRES 22 B 336 LEU PHE GLY PHE SER SER TYR VAL THR ASN ILE MET ASP SEQRES 23 B 336 VAL MET ASP ARG VAL ASN PRO ASP GLY MET ALA PHE ILE SEQRES 24 B 336 PRO LEU ARG VAL ILE PRO PHE LEU ARG GLU LYS GLY VAL SEQRES 25 B 336 PRO GLN GLU THR LEU ALA GLY ILE THR VAL THR ASN PRO SEQRES 26 B 336 ALA ARG PHE LEU SER PRO THR LEU ARG ALA SER MODRES 1QW7 KCX A 169 LYS LYSINE NZ-CARBOXYLIC ACID MODRES 1QW7 KCX B 169 LYS LYSINE NZ-CARBOXYLIC ACID HET KCX A 169 12 HET KCX B 169 12 HET CO A 601 1 HET CO A 602 1 HET NA A 605 1 HET EBP A 702 16 HET CO B 603 1 HET CO B 604 1 HET NA B 606 1 HET EBP B 701 16 HETNAM KCX LYSINE NZ-CARBOXYLIC ACID HETNAM CO COBALT (II) ION HETNAM NA SODIUM ION HETNAM EBP DIETHYL 4-METHYLBENZYLPHOSPHONATE FORMUL 1 KCX 2(C7 H14 N2 O4) FORMUL 3 CO 4(CO 2+) FORMUL 5 NA 2(NA 1+) FORMUL 6 EBP 2(C12 H19 O3 P) FORMUL 11 HOH *525(H2 O) HELIX 1 1 ILE A 46 GLY A 50 1 5 HELIX 2 2 GLY A 64 TRP A 69 1 6 HELIX 3 3 PRO A 70 GLY A 74 5 5 HELIX 4 4 SER A 75 ALA A 93 1 19 HELIX 5 5 THR A 103 GLY A 107 5 5 HELIX 6 6 ASP A 109 ASP A 121 1 13 HELIX 7 7 PRO A 135 LEU A 140 1 6 HELIX 8 8 SER A 142 TYR A 156 1 15 HELIX 9 9 THR A 177 GLY A 195 1 19 HELIX 10 10 ALA A 203 GLN A 206 5 4 HELIX 11 11 ARG A 207 GLU A 219 1 13 HELIX 12 12 SER A 222 SER A 224 5 3 HELIX 13 13 HIS A 230 THR A 234 5 5 HELIX 14 14 ASP A 236 ARG A 246 1 11 HELIX 15 15 ASN A 265 GLY A 273 1 9 HELIX 16 16 SER A 276 GLN A 290 1 15 HELIX 17 17 TYR A 292 LYS A 294 5 3 HELIX 18 18 ASN A 312 ASN A 321 1 10 HELIX 19 19 ASP A 323 MET A 325 5 3 HELIX 20 20 ALA A 326 ARG A 331 1 6 HELIX 21 21 ARG A 331 LYS A 339 1 9 HELIX 22 22 PRO A 342 VAL A 351 1 10 HELIX 23 23 VAL A 351 SER A 359 1 9 HELIX 24 24 ILE B 46 GLY B 50 1 5 HELIX 25 25 GLY B 64 TRP B 69 1 6 HELIX 26 26 PRO B 70 GLY B 74 5 5 HELIX 27 27 SER B 75 ALA B 93 1 19 HELIX 28 28 THR B 103 GLY B 107 5 5 HELIX 29 29 ASP B 109 ASP B 121 1 13 HELIX 30 30 PRO B 135 LEU B 140 1 6 HELIX 31 31 SER B 142 TYR B 156 1 15 HELIX 32 32 THR B 177 GLY B 195 1 19 HELIX 33 33 ALA B 203 GLN B 206 5 4 HELIX 34 34 ARG B 207 GLU B 219 1 13 HELIX 35 35 SER B 222 SER B 224 5 3 HELIX 36 36 HIS B 230 THR B 234 5 5 HELIX 37 37 ASP B 236 ARG B 246 1 11 HELIX 38 38 ASN B 265 GLY B 273 1 9 HELIX 39 39 SER B 276 GLN B 290 1 15 HELIX 40 40 TYR B 292 LYS B 294 5 3 HELIX 41 41 ASN B 312 ASN B 321 1 10 HELIX 42 42 ASP B 323 MET B 325 5 3 HELIX 43 43 ALA B 326 ARG B 331 1 6 HELIX 44 44 ARG B 331 LYS B 339 1 9 HELIX 45 45 PRO B 342 VAL B 351 1 10 HELIX 46 46 VAL B 351 SER B 359 1 9 SHEET 1 A 2 ILE A 31 GLY A 32 0 SHEET 2 A 2 THR A 361 LEU A 362 -1 O LEU A 362 N ILE A 31 SHEET 1 B 2 ARG A 36 THR A 39 0 SHEET 2 B 2 GLY A 42 THR A 45 -1 O ILE A 44 N ILE A 37 SHEET 1 C 3 THR A 52 GLU A 56 0 SHEET 2 C 3 THR A 97 ASP A 100 1 O VAL A 99 N LEU A 53 SHEET 3 C 3 HIS A 123 VAL A 125 1 O VAL A 125 N ILE A 98 SHEET 1 D 6 ALA A 127 GLY A 129 0 SHEET 2 D 6 ILE A 167 ALA A 171 1 O KCX A 169 N THR A 128 SHEET 3 D 6 VAL A 198 HIS A 201 1 O THR A 199 N ILE A 168 SHEET 4 D 6 VAL A 226 ILE A 228 1 O CYS A 227 N THR A 200 SHEET 5 D 6 LEU A 249 LEU A 252 1 O LEU A 249 N ILE A 228 SHEET 6 D 6 ILE A 296 VAL A 298 1 O LEU A 297 N LEU A 252 SHEET 1 E 2 ILE B 31 GLY B 32 0 SHEET 2 E 2 THR B 361 LEU B 362 -1 O LEU B 362 N ILE B 31 SHEET 1 F 2 ARG B 36 THR B 39 0 SHEET 2 F 2 GLY B 42 THR B 45 -1 O ILE B 44 N ILE B 37 SHEET 1 G 3 THR B 52 GLU B 56 0 SHEET 2 G 3 THR B 97 ASP B 100 1 O VAL B 99 N GLU B 56 SHEET 3 G 3 HIS B 123 VAL B 125 1 O HIS B 123 N ILE B 98 SHEET 1 H 2 CYS B 59 GLY B 60 0 SHEET 2 H 2 GLY B 305 PHE B 306 1 O GLY B 305 N GLY B 60 SHEET 1 I 6 ALA B 127 GLY B 129 0 SHEET 2 I 6 ILE B 167 ALA B 171 1 O KCX B 169 N THR B 128 SHEET 3 I 6 VAL B 198 HIS B 201 1 O THR B 199 N ILE B 168 SHEET 4 I 6 VAL B 226 ILE B 228 1 O CYS B 227 N THR B 200 SHEET 5 I 6 LEU B 249 LEU B 252 1 O LEU B 249 N ILE B 228 SHEET 6 I 6 ILE B 296 VAL B 298 1 O LEU B 297 N LEU B 252 LINK C ILE A 168 N KCX A 169 1555 1555 1.34 LINK C KCX A 169 N VAL A 170 1555 1555 1.33 LINK C ILE B 168 N KCX B 169 1555 1555 1.33 LINK C KCX B 169 N VAL B 170 1555 1555 1.33 LINK OD1 ASN A 38 NA NA A 605 1555 1555 2.76 LINK NE2 HIS A 55 CO CO A 602 1555 1555 2.20 LINK NE2 HIS A 57 CO CO A 602 1555 1555 2.10 LINK O ILE A 154 NA NA A 605 1555 1555 2.81 LINK OQ1 KCX A 169 CO CO A 601 1555 1555 1.93 LINK OQ2 KCX A 169 CO CO A 602 1555 1555 2.14 LINK ND1 HIS A 201 CO CO A 601 1555 1555 2.13 LINK NE2 HIS A 230 CO CO A 601 1555 1555 2.18 LINK OD2 ASP A 301 CO CO A 602 1555 1555 2.29 LINK CO CO A 601 O HOH A 802 1555 1555 1.81 LINK CO CO A 601 O HOH A 826 1555 1555 2.00 LINK CO CO A 602 O HOH A 802 1555 1555 2.09 LINK NA NA A 605 O HOH A 913 1555 1555 2.77 LINK OD1 ASN B 38 NA NA B 606 1555 1555 2.73 LINK NE2 HIS B 55 CO CO B 603 1555 1555 2.10 LINK NE2 HIS B 57 CO CO B 603 1555 1555 2.01 LINK O ILE B 154 NA NA B 606 1555 1555 2.72 LINK OQ2 KCX B 169 CO CO B 603 1555 1555 2.26 LINK OQ1 KCX B 169 CO CO B 604 1555 1555 2.14 LINK ND1 HIS B 201 CO CO B 604 1555 1555 2.17 LINK NE2 HIS B 230 CO CO B 604 1555 1555 2.14 LINK OD2 ASP B 301 CO CO B 603 1555 1555 2.37 LINK CO CO B 603 O HOH B 774 1555 1555 2.40 LINK CO CO B 604 O HOH B 774 1555 1555 1.65 LINK CO CO B 604 O HOH B 776 1555 1555 1.85 LINK NA NA B 606 O HOH B 802 1555 1555 2.81 LINK NA NA B 606 O HOH B 830 1555 1555 2.59 SITE 1 AC1 7 KCX A 169 HIS A 201 HIS A 230 ARG A 254 SITE 2 AC1 7 CO A 602 HOH A 802 HOH A 826 SITE 1 AC2 6 HIS A 55 HIS A 57 KCX A 169 ASP A 301 SITE 2 AC2 6 CO A 601 HOH A 802 SITE 1 AC3 6 HIS B 55 HIS B 57 KCX B 169 ASP B 301 SITE 2 AC3 6 CO B 604 HOH B 774 SITE 1 AC4 7 KCX B 169 HIS B 201 HIS B 230 ARG B 254 SITE 2 AC4 7 CO B 603 HOH B 774 HOH B 776 SITE 1 AC5 4 ASN A 38 ILE A 154 HOH A 913 HOH B 719 SITE 1 AC6 4 ASN B 38 ILE B 154 HOH B 802 HOH B 830 SITE 1 AC7 4 GLN A 155 TYR A 156 GLU B 71 THR B 350 SITE 1 AC8 6 PHE A 51 GLU A 71 HOH A 969 GLN B 155 SITE 2 AC8 6 TYR B 156 ARG B 164 CRYST1 126.719 89.879 68.337 90.00 91.73 90.00 C 1 2 1 8 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 0.007891 0.000000 0.000239 0.00000 SCALE2 0.000000 0.011126 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014640 0.00000