HEADER HYDROLASE 23-JUN-09 3A3W TITLE STRUCTURE OF OPDA MUTANT TITLE 2 (G60A/A80V/S92A/R118Q/K185R/Q206P/D208G/I260T/G273S) WITH DIETHYL 4- TITLE 3 METHOXYPHENYL PHOSPHATE BOUND IN THE ACTIVE SITE COMPND MOL_ID: 1; COMPND 2 MOLECULE: PHOSPHOTRIESTERASE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 32-360; COMPND 5 EC: 3.1.8.1; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: AGROBACTERIUM TUMEFACIENS; SOURCE 3 ORGANISM_TAXID: 358; SOURCE 4 GENE: OPDA; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3)RECA-; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PETMCSI KEYWDS PHOSPHOTRIESTERASE, OPDA, METALLOENZYME, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR D.L.OLLIS,D.S.TAWFIK,G.SCHENK,C.J.JACKSON,J.L.FOO,N.TOKURIKI, AUTHOR 2 L.AFRIAT,P.D.CARR,H.K.KIM REVDAT 4 15-NOV-23 3A3W 1 REMARK REVDAT 3 01-NOV-23 3A3W 1 REMARK REVDAT 2 10-NOV-21 3A3W 1 REMARK SEQADV LINK REVDAT 1 12-JAN-10 3A3W 0 JRNL AUTH C.J.JACKSON,J.-L.FOO,N.TOKURIKI,L.AFRIAT,P.D.CARR,H.-K.KIM, JRNL AUTH 2 G.SCHENK,D.S.TAWFIK,D.L.OLLIS JRNL TITL CONFORMATIONAL SAMPLING, CATALYSIS, AND EVOLUTION OF THE JRNL TITL 2 BACTERIAL PHOSPHOTRIESTERASE JRNL REF PROC.NATL.ACAD.SCI.USA 2009 JRNL REFN ESSN 1091-6490 JRNL PMID 19966226 JRNL DOI 10.1073/PNAS.0907548106 REMARK 2 REMARK 2 RESOLUTION. 1.85 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0088 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) : 1.85 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.80 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 3 NUMBER OF REFLECTIONS : 34885 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) : 0.176 REMARK 3 R VALUE (WORKING SET) : 0.174 REMARK 3 FREE R VALUE : 0.209 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.700 REMARK 3 FREE R VALUE TEST SET COUNT : 1715 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) : 1.85 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.90 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2324 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 92.18 REMARK 3 BIN R VALUE (WORKING SET) : 0.2590 REMARK 3 BIN FREE R VALUE SET COUNT : 116 REMARK 3 BIN FREE R VALUE : 0.3390 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2509 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 19 REMARK 3 SOLVENT ATOMS : 283 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 25.00 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.31000 REMARK 3 B22 (A**2) : -1.31000 REMARK 3 B33 (A**2) : 1.96000 REMARK 3 B12 (A**2) : -0.65000 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): 0.113 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.112 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.088 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.976 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.961 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.945 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2590 ; 0.017 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3518 ; 1.624 ; 1.967 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 328 ; 6.888 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 107 ;29.921 ;21.963 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 404 ;15.315 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 26 ;18.385 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 404 ; 0.108 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1958 ; 0.006 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1406 ; 0.238 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1786 ; 0.305 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 267 ; 0.157 ; 0.200 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): 51 ; 0.174 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 22 ; 0.236 ; 0.200 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): 1678 ; 1.008 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2634 ; 1.621 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1022 ; 2.494 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 884 ; 4.066 ; 4.500 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): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 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 3A3W COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 24-JUN-09. REMARK 100 THE DEPOSITION ID IS D_1000028778. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 13-NOV-07 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRL REMARK 200 BEAMLINE : BL9-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.975 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL MONOCHROMATOR REMARK 200 OPTICS : FLAT COLLIMATING MIRROR, DOUBLE REMARK 200 CRYSTAL MONOCHROMATOR, TOROID REMARK 200 FOCUSING MIRROR REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 325 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 43843 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 REMARK 200 RESOLUTION RANGE LOW (A) : 40.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 92.4 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.76 REMARK 200 COMPLETENESS FOR SHELL (%) : 51.9 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: PDB ENTRY 2D2J REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 59.23 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.02 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% PEG3350, 0.2M NANO3, PH7, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 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+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+2/3 REMARK 290 6555 -X,-X+Y,-Z+1/3 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 20.89633 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 41.79267 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 41.79267 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 20.89633 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: 22320 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -47.0 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 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 CB VAL A 116 O HOH A 597 1.97 REMARK 500 O SER A 203 O HOH A 555 2.15 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 552 O HOH A 552 4555 2.11 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 139 NE - CZ - NH1 ANGL. DEV. = 4.6 DEGREES REMARK 500 ARG A 139 NE - CZ - NH2 ANGL. DEV. = -3.8 DEGREES REMARK 500 ARG A 225 NE - CZ - NH2 ANGL. DEV. = -3.2 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 SER A 61 -143.56 -141.34 REMARK 500 TRP A 131 -157.59 -96.37 REMARK 500 TRP A 131 -153.57 -96.37 REMARK 500 GLU A 159 -128.39 51.79 REMARK 500 SER A 205 97.26 22.43 REMARK 500 PRO A 206 -66.55 25.46 REMARK 500 ASP A 235 35.55 -94.60 REMARK 500 PHE A 306 78.97 -154.80 REMARK 500 VAL A 351 -56.84 -123.42 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 SER A 205 PRO A 206 53.45 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 CO A 800 CO REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 55 NE2 REMARK 620 2 HIS A 57 NE2 115.2 REMARK 620 3 KCX A 169 OQ2 94.3 87.7 REMARK 620 4 ASP A 301 OD1 87.1 90.7 178.2 REMARK 620 5 HOH A 612 O 108.0 136.8 89.6 91.0 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CO A 801 CO REMARK 620 N RES CSSEQI ATOM REMARK 620 1 KCX A 169 OQ1 REMARK 620 2 HIS A 201 ND1 104.9 REMARK 620 3 HIS A 230 NE2 106.2 87.1 REMARK 620 4 HOH A 612 O 96.5 153.6 101.8 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 CO A 800 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CO A 801 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EPL A 701 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3A3X RELATED DB: PDB REMARK 900 STRUCTURE OF OPDA MUTANT (G60A/A80V/S92A/R118Q/K185R/Q206P/D208G/ REMARK 900 I260T/G273S) DBREF 3A3W A 33 361 UNP Q93LD7 Q93LD7_9RHIZ 32 360 SEQADV 3A3W ALA A 60 UNP Q93LD7 GLY 59 ENGINEERED MUTATION SEQADV 3A3W VAL A 80 UNP Q93LD7 ALA 79 ENGINEERED MUTATION SEQADV 3A3W ALA A 92 UNP Q93LD7 SER 91 ENGINEERED MUTATION SEQADV 3A3W GLN A 118 UNP Q93LD7 ARG 117 ENGINEERED MUTATION SEQADV 3A3W ARG A 185 UNP Q93LD7 LYS 184 ENGINEERED MUTATION SEQADV 3A3W PRO A 206 UNP Q93LD7 GLN 205 ENGINEERED MUTATION SEQADV 3A3W GLY A 208 UNP Q93LD7 ASP 207 ENGINEERED MUTATION SEQADV 3A3W THR A 260 UNP Q93LD7 ILE 259 ENGINEERED MUTATION SEQADV 3A3W SER A 273 UNP Q93LD7 GLY 272 ENGINEERED MUTATION SEQRES 1 A 329 THR GLY ASP LEU ILE ASN THR VAL ARG GLY PRO ILE PRO SEQRES 2 A 329 VAL SER GLU ALA GLY PHE THR LEU THR HIS GLU HIS ILE SEQRES 3 A 329 CYS ALA SER SER ALA GLY PHE LEU ARG ALA TRP PRO GLU SEQRES 4 A 329 PHE PHE GLY SER ARG LYS ALA LEU VAL GLU LYS ALA VAL SEQRES 5 A 329 ARG GLY LEU ARG HIS ALA ARG ALA ALA GLY VAL GLN THR SEQRES 6 A 329 ILE VAL ASP VAL SER THR PHE ASP ILE GLY ARG ASP VAL SEQRES 7 A 329 ARG LEU LEU ALA GLU VAL SER GLN ALA ALA ASP VAL HIS SEQRES 8 A 329 ILE VAL ALA ALA THR GLY LEU TRP PHE ASP PRO PRO LEU SEQRES 9 A 329 SER MET ARG MET ARG SER VAL GLU GLU LEU THR GLN PHE SEQRES 10 A 329 PHE LEU ARG GLU ILE GLN HIS GLY ILE GLU ASP THR GLY SEQRES 11 A 329 ILE ARG ALA GLY ILE ILE KCX VAL ALA THR THR GLY LYS SEQRES 12 A 329 ALA THR PRO PHE GLN GLU LEU VAL LEU ARG ALA ALA ALA SEQRES 13 A 329 ARG ALA SER LEU ALA THR GLY VAL PRO VAL THR THR HIS SEQRES 14 A 329 THR SER ALA SER PRO ARG GLY GLY GLU GLN GLN ALA ALA SEQRES 15 A 329 ILE PHE GLU SER GLU GLY LEU SER PRO SER ARG VAL CYS SEQRES 16 A 329 ILE GLY HIS SER ASP ASP THR ASP ASP LEU SER TYR LEU SEQRES 17 A 329 THR GLY LEU ALA ALA ARG GLY TYR LEU VAL GLY LEU ASP SEQRES 18 A 329 ARG MET PRO TYR SER ALA THR GLY LEU GLU GLY ASN ALA SEQRES 19 A 329 SER ALA LEU ALA LEU PHE SER THR ARG SER TRP GLN THR SEQRES 20 A 329 ARG ALA LEU LEU ILE LYS ALA LEU ILE ASP ARG GLY TYR SEQRES 21 A 329 LYS ASP ARG ILE LEU VAL SER HIS ASP TRP LEU PHE GLY SEQRES 22 A 329 PHE SER SER TYR VAL THR ASN ILE MET ASP VAL MET ASP SEQRES 23 A 329 ARG ILE ASN PRO ASP GLY MET ALA PHE VAL PRO LEU ARG SEQRES 24 A 329 VAL ILE PRO PHE LEU ARG GLU LYS GLY VAL PRO PRO GLU SEQRES 25 A 329 THR LEU ALA GLY VAL THR VAL ALA ASN PRO ALA ARG PHE SEQRES 26 A 329 LEU SER PRO THR MODRES 3A3W KCX A 169 LYS LYSINE NZ-CARBOXYLIC ACID HET KCX A 169 12 HET CO A 800 1 HET CO A 801 1 HET EPL A 701 17 HETNAM KCX LYSINE NZ-CARBOXYLIC ACID HETNAM CO COBALT (II) ION HETNAM EPL DIETHYL 4-METHOXYPHENYL PHOSPHATE FORMUL 1 KCX C7 H14 N2 O4 FORMUL 2 CO 2(CO 2+) FORMUL 4 EPL C11 H17 O5 P FORMUL 5 HOH *283(H2 O) HELIX 1 1 SER A 47 ALA A 49 5 3 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 MET A 140 1 6 HELIX 8 8 SER A 142 HIS A 156 1 15 HELIX 9 9 THR A 177 GLY A 195 1 19 HELIX 10 10 GLY A 208 GLU A 219 1 12 HELIX 11 11 SER A 222 SER A 224 5 3 HELIX 12 12 HIS A 230 THR A 234 5 5 HELIX 13 13 ASP A 236 ARG A 246 1 11 HELIX 14 14 ASN A 265 PHE A 272 1 8 HELIX 15 15 SER A 276 ARG A 290 1 15 HELIX 16 16 TYR A 292 ASP A 294 5 3 HELIX 17 17 ASN A 312 ASN A 321 1 10 HELIX 18 18 ASP A 323 MET A 325 5 3 HELIX 19 19 ALA A 326 ARG A 331 1 6 HELIX 20 20 ARG A 331 LYS A 339 1 9 HELIX 21 21 PRO A 342 VAL A 351 1 10 HELIX 22 22 VAL A 351 SER A 359 1 9 SHEET 1 A 2 LEU A 36 THR A 39 0 SHEET 2 A 2 GLY A 42 PRO A 45 -1 O ILE A 44 N ILE A 37 SHEET 1 B 3 THR A 52 GLU A 56 0 SHEET 2 B 3 THR A 97 ASP A 100 1 O VAL A 99 N LEU A 53 SHEET 3 B 3 HIS A 123 VAL A 125 1 O VAL A 125 N ASP A 100 SHEET 1 C 2 CYS A 59 ALA A 60 0 SHEET 2 C 2 GLY A 305 PHE A 306 1 O GLY A 305 N ALA A 60 SHEET 1 D 6 ALA A 127 LEU A 130 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 VAL A 198 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 LINK C ILE A 168 N KCX A 169 1555 1555 1.46 LINK C KCX A 169 N VAL A 170 1555 1555 1.40 LINK NE2 HIS A 55 CO CO A 800 1555 1555 2.15 LINK NE2 HIS A 57 CO CO A 800 1555 1555 2.09 LINK OQ2 KCX A 169 CO CO A 800 1555 1555 2.22 LINK OQ1 KCX A 169 CO CO A 801 1555 1555 2.02 LINK ND1 HIS A 201 CO CO A 801 1555 1555 2.15 LINK NE2 HIS A 230 CO CO A 801 1555 1555 2.06 LINK OD1 ASP A 301 CO CO A 800 1555 1555 2.17 LINK O HOH A 612 CO CO A 800 1555 1555 1.99 LINK O HOH A 612 CO CO A 801 1555 1555 2.24 CISPEP 1 PRO A 206 ARG A 207 0 -17.39 SITE 1 AC1 7 HIS A 55 HIS A 57 KCX A 169 ASP A 301 SITE 2 AC1 7 HOH A 612 EPL A 701 CO A 801 SITE 1 AC2 6 KCX A 169 HIS A 201 HIS A 230 ARG A 254 SITE 2 AC2 6 HOH A 612 CO A 800 SITE 1 AC3 9 HIS A 57 TRP A 131 MET A 140 ARG A 254 SITE 2 AC3 9 TYR A 257 ASP A 301 PHE A 306 SER A 308 SITE 3 AC3 9 CO A 800 CRYST1 109.011 109.011 62.689 90.00 90.00 120.00 P 31 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 0.009173 0.005296 0.000000 0.00000 SCALE2 0.000000 0.010593 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015952 0.00000