HEADER HYDROLASE 26-FEB-18 6FU6 TITLE PHOSPHOTRIESTERASE PTE_C23_2 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 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BREVUNDIMONAS DIMINUTA; SOURCE 3 ORGANISM_COMMON: PSEUDOMONAS DIMINUTA; SOURCE 4 ORGANISM_TAXID: 293; SOURCE 5 GENE: OPD; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS METALLOENZYME, TIM BARREL, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR O.DYM,N.AGGARWAL,S.ALBECK,T.UNGER,S.HAMER ROGOTNER,I.SILMAN,H.LEADER, AUTHOR 2 Y.ASHANI,M.GOLDSMITH,P.GREISEN,D.TAWFIK,L.J.SUSSMAN REVDAT 2 17-JAN-24 6FU6 1 LINK REVDAT 1 20-MAR-19 6FU6 0 JRNL AUTH O.DYM,N.AGGARWAL,S.ALBECK,T.UNGER,S.HAMER ROGOTNER,I.SILMAN, JRNL AUTH 2 H.LEADER,Y.ASHANI,M.GOLDSMITH,P.GREISEN,D.TAWFIK,L.J.SUSSMAN JRNL TITL PHOSPHOTRIESTERASE PTE_A53_4 JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.95 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0189 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.95 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 70.41 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 42615 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) : 0.158 REMARK 3 R VALUE (WORKING SET) : 0.156 REMARK 3 FREE R VALUE : 0.199 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2264 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) : 1.95 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.00 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3097 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.2110 REMARK 3 BIN FREE R VALUE SET COUNT : 175 REMARK 3 BIN FREE R VALUE : 0.2590 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4977 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 31 REMARK 3 SOLVENT ATOMS : 290 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 18.32 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 18.57 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.88000 REMARK 3 B22 (A**2) : 0.18000 REMARK 3 B33 (A**2) : -1.12000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.43000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.155 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.139 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.098 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.461 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.959 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.939 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5142 ; 0.018 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 4847 ; 0.003 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6976 ; 1.865 ; 1.963 REMARK 3 BOND ANGLES OTHERS (DEGREES): 11158 ; 1.229 ; 3.001 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 662 ; 6.520 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 214 ;32.208 ;22.617 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 830 ;13.026 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 50 ;17.607 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 813 ; 0.110 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 5786 ; 0.009 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 1088 ; 0.002 ; 0.020 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): 2642 ; 1.362 ; 1.705 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 2643 ; 1.362 ; 1.705 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3306 ; 1.952 ; 2.547 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 3307 ; 1.955 ; 2.549 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2500 ; 2.265 ; 1.988 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 2498 ; 2.257 ; 1.988 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 3670 ; 3.515 ; 2.885 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 5891 ; 4.656 ;21.341 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 5844 ; 4.623 ;21.252 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 : NULL 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 6FU6 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 26-FEB-18. REMARK 100 THE DEPOSITION ID IS D_1200008936. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 25-MAY-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU RUH3R REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5415 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV++ REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 44881 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.950 REMARK 200 RESOLUTION RANGE LOW (A) : 70.410 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 6.100 REMARK 200 R MERGE (I) : 0.05192 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.8400 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.95 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.02 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.24800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.180 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 1HYZ REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.60 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.18 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.05M HEPES PH=7.5 13% POLYACRYLIC REMARK 280 ACID 5100 NA 0.01M MGCL2, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 40.58000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2990 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 22990 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -88.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 GLY A 34 REMARK 465 LEU A 362 REMARK 465 ARG A 363 REMARK 465 ALA A 364 REMARK 465 SER A 365 REMARK 465 GLY B 34 REMARK 465 ASP B 35 REMARK 465 SER B 365 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 GLU A 81 CD OE1 OE2 REMARK 470 ARG A 89 CZ NH1 NH2 REMARK 470 ARG B 363 CZ NH1 NH2 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 NZ LYS A 169 O2 FMT A 401 2.11 REMARK 500 O31 TA8 A 404 O HOH A 501 2.15 REMARK 500 NZ LYS B 169 O2 FMT B 402 2.18 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 71 CD GLU A 71 OE2 -0.069 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 96 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 ARG A 139 NE - CZ - NH1 ANGL. DEV. = 5.0 DEGREES REMARK 500 ARG A 139 NE - CZ - NH2 ANGL. DEV. = -3.9 DEGREES REMARK 500 ARG A 152 NE - CZ - NH1 ANGL. DEV. = 4.1 DEGREES REMARK 500 ARG A 152 NE - CZ - NH2 ANGL. DEV. = -3.9 DEGREES REMARK 500 ARG A 185 NE - CZ - NH1 ANGL. DEV. = 4.5 DEGREES REMARK 500 ARG A 225 NE - CZ - NH1 ANGL. DEV. = 5.2 DEGREES REMARK 500 ARG A 225 NE - CZ - NH2 ANGL. DEV. = -6.6 DEGREES REMARK 500 ASP A 301 CB - CG - OD1 ANGL. DEV. = 6.2 DEGREES REMARK 500 PHE A 306 CB - CG - CD1 ANGL. DEV. = 4.9 DEGREES REMARK 500 ARG B 96 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 ARG B 152 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 ARG B 152 NE - CZ - NH2 ANGL. DEV. = -3.5 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 -141.42 -145.00 REMARK 500 TRP A 69 58.84 -146.63 REMARK 500 THR A 128 -168.61 -107.72 REMARK 500 TRP A 131 -154.48 -105.53 REMARK 500 GLU A 159 -134.05 51.76 REMARK 500 SER B 61 -142.66 -142.22 REMARK 500 THR B 128 -166.04 -116.02 REMARK 500 TRP B 131 -152.46 -100.16 REMARK 500 GLU B 159 -129.26 56.53 REMARK 500 TYR B 309 -159.28 -141.33 REMARK 500 REMARK 500 REMARK: NULL REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 TA8 A 404 REMARK 610 TA8 B 405 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 ZN A 402 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 55 NE2 REMARK 620 2 HIS A 57 NE2 121.9 REMARK 620 3 ASP A 301 OD1 86.0 95.6 REMARK 620 4 FMT A 401 O1 97.3 82.5 176.7 REMARK 620 5 TA8 A 404 O41 116.0 121.8 94.5 84.4 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 403 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 201 ND1 REMARK 620 2 HIS A 230 NE2 102.1 REMARK 620 3 FMT A 401 O2 108.5 114.6 REMARK 620 4 TA8 A 404 O42 96.0 127.8 104.9 REMARK 620 5 TA8 A 404 O41 151.3 91.0 88.4 56.6 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 403 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 55 NE2 REMARK 620 2 HIS B 57 NE2 118.8 REMARK 620 3 ASP B 301 OD1 88.5 94.0 REMARK 620 4 FMT B 402 O1 92.6 86.3 178.5 REMARK 620 5 TA8 B 405 O42 115.7 125.0 94.4 84.2 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 404 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 201 ND1 REMARK 620 2 HIS B 230 NE2 99.0 REMARK 620 3 FMT B 402 O2 108.0 112.2 REMARK 620 4 TA8 B 405 O41 95.6 124.1 113.7 REMARK 620 5 TA8 B 405 O42 152.3 89.3 92.8 58.6 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 FMT A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue TA8 A 404 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN B 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN B 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN B 404 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue TA8 B 405 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for Di-peptide FMT B 402 and LYS B REMARK 800 169 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 6FEE RELATED DB: PDB REMARK 900 RELATED ID: 6FEF RELATED DB: PDB REMARK 900 RELATED ID: 6FEI RELATED DB: PDB REMARK 900 RELATED ID: 6FEV RELATED DB: PDB REMARK 900 RELATED ID: 6FFW RELATED DB: PDB REMARK 900 RELATED ID: 6FOR RELATED DB: PDB REMARK 900 RELATED ID: 6FRZ RELATED DB: PDB REMARK 900 RELATED ID: 6FQE RELATED DB: PDB REMARK 900 RELATED ID: 6FS3 RELATED DB: PDB REMARK 900 RELATED ID: 6FU0 RELATED DB: PDB DBREF 6FU6 A 34 365 UNP P0A434 OPD_BREDI 34 365 DBREF 6FU6 B 34 365 UNP P0A434 OPD_BREDI 34 365 SEQADV 6FU6 ALA A 77 UNP P0A434 LYS 77 CONFLICT SEQADV 6FU6 VAL A 80 UNP P0A434 ALA 80 CONFLICT SEQADV 6FU6 GLU A 132 UNP P0A434 PHE 132 CONFLICT SEQADV 6FU6 ASN A 173 UNP P0A434 THR 173 CONFLICT SEQADV 6FU6 ARG A 185 UNP P0A434 LYS 185 CONFLICT SEQADV 6FU6 GLY A 254 UNP P0A434 HIS 254 CONFLICT SEQADV 6FU6 ASN A 274 UNP P0A434 ILE 274 CONFLICT SEQADV 6FU6 SER A 319 UNP P0A434 ARG 319 CONFLICT SEQADV 6FU6 SER A 342 UNP P0A434 PRO 342 CONFLICT SEQADV 6FU6 ALA B 77 UNP P0A434 LYS 77 CONFLICT SEQADV 6FU6 VAL B 80 UNP P0A434 ALA 80 CONFLICT SEQADV 6FU6 GLU B 132 UNP P0A434 PHE 132 CONFLICT SEQADV 6FU6 ASN B 173 UNP P0A434 THR 173 CONFLICT SEQADV 6FU6 ARG B 185 UNP P0A434 LYS 185 CONFLICT SEQADV 6FU6 GLY B 254 UNP P0A434 HIS 254 CONFLICT SEQADV 6FU6 ASN B 274 UNP P0A434 ILE 274 CONFLICT SEQADV 6FU6 SER B 319 UNP P0A434 ARG 319 CONFLICT SEQADV 6FU6 SER B 342 UNP P0A434 PRO 342 CONFLICT SEQRES 1 A 332 GLY ASP ARG ILE ASN THR VAL ARG GLY PRO ILE THR ILE SEQRES 2 A 332 SER GLU ALA GLY PHE THR LEU THR HIS GLU HIS ILE CYS SEQRES 3 A 332 GLY SER SER ALA GLY PHE LEU ARG ALA TRP PRO GLU PHE SEQRES 4 A 332 PHE GLY SER ARG ALA ALA LEU VAL GLU LYS ALA VAL ARG SEQRES 5 A 332 GLY LEU ARG ARG ALA ARG ALA ALA GLY VAL ARG THR ILE SEQRES 6 A 332 VAL ASP VAL SER THR PHE ASP ILE GLY ARG ASP VAL SER SEQRES 7 A 332 LEU LEU ALA GLU VAL SER ARG ALA ALA ASP VAL HIS ILE SEQRES 8 A 332 VAL ALA ALA THR GLY LEU TRP GLU ASP PRO PRO LEU SER SEQRES 9 A 332 MET ARG LEU ARG SER VAL GLU GLU LEU THR GLN PHE PHE SEQRES 10 A 332 LEU ARG GLU ILE GLN TYR GLY ILE GLU ASP THR GLY ILE SEQRES 11 A 332 ARG ALA GLY ILE ILE LYS VAL ALA THR ASN GLY LYS ALA SEQRES 12 A 332 THR PRO PHE GLN GLU LEU VAL LEU ARG ALA ALA ALA ARG SEQRES 13 A 332 ALA SER LEU ALA THR GLY VAL PRO VAL THR THR HIS THR SEQRES 14 A 332 ALA ALA SER GLN ARG ASP GLY GLU GLN GLN ALA ALA ILE SEQRES 15 A 332 PHE GLU SER GLU GLY LEU SER PRO SER ARG VAL CYS ILE SEQRES 16 A 332 GLY HIS SER ASP ASP THR ASP ASP LEU SER TYR LEU THR SEQRES 17 A 332 ALA LEU ALA ALA ARG GLY TYR LEU ILE GLY LEU ASP GLY SEQRES 18 A 332 ILE PRO HIS SER ALA ILE GLY LEU GLU ASP ASN ALA SER SEQRES 19 A 332 ALA SER ALA LEU LEU GLY ASN ARG SER TRP GLN THR ARG SEQRES 20 A 332 ALA LEU LEU ILE LYS ALA LEU ILE ASP GLN GLY TYR MET SEQRES 21 A 332 LYS GLN ILE LEU VAL SER ASN ASP TRP LEU PHE GLY PHE SEQRES 22 A 332 SER SER TYR VAL THR ASN ILE MET ASP VAL MET ASP SER SEQRES 23 A 332 VAL ASN PRO ASP GLY MET ALA PHE ILE PRO LEU ARG VAL SEQRES 24 A 332 ILE PRO PHE LEU ARG GLU LYS GLY VAL SER GLN GLU THR SEQRES 25 A 332 LEU ALA GLY ILE THR VAL THR ASN PRO ALA ARG PHE LEU SEQRES 26 A 332 SER PRO THR LEU ARG ALA SER SEQRES 1 B 332 GLY ASP ARG ILE ASN THR VAL ARG GLY PRO ILE THR ILE SEQRES 2 B 332 SER GLU ALA GLY PHE THR LEU THR HIS GLU HIS ILE CYS SEQRES 3 B 332 GLY SER SER ALA GLY PHE LEU ARG ALA TRP PRO GLU PHE SEQRES 4 B 332 PHE GLY SER ARG ALA ALA LEU VAL GLU LYS ALA VAL ARG SEQRES 5 B 332 GLY LEU ARG ARG ALA ARG ALA ALA GLY VAL ARG THR ILE SEQRES 6 B 332 VAL ASP VAL SER THR PHE ASP ILE GLY ARG ASP VAL SER SEQRES 7 B 332 LEU LEU ALA GLU VAL SER ARG ALA ALA ASP VAL HIS ILE SEQRES 8 B 332 VAL ALA ALA THR GLY LEU TRP GLU ASP PRO PRO LEU SER SEQRES 9 B 332 MET ARG LEU ARG SER VAL GLU GLU LEU THR GLN PHE PHE SEQRES 10 B 332 LEU ARG GLU ILE GLN TYR GLY ILE GLU ASP THR GLY ILE SEQRES 11 B 332 ARG ALA GLY ILE ILE LYS VAL ALA THR ASN GLY LYS ALA SEQRES 12 B 332 THR PRO PHE GLN GLU LEU VAL LEU ARG ALA ALA ALA ARG SEQRES 13 B 332 ALA SER LEU ALA THR GLY VAL PRO VAL THR THR HIS THR SEQRES 14 B 332 ALA ALA SER GLN ARG ASP GLY GLU GLN GLN ALA ALA ILE SEQRES 15 B 332 PHE GLU SER GLU GLY LEU SER PRO SER ARG VAL CYS ILE SEQRES 16 B 332 GLY HIS SER ASP ASP THR ASP ASP LEU SER TYR LEU THR SEQRES 17 B 332 ALA LEU ALA ALA ARG GLY TYR LEU ILE GLY LEU ASP GLY SEQRES 18 B 332 ILE PRO HIS SER ALA ILE GLY LEU GLU ASP ASN ALA SER SEQRES 19 B 332 ALA SER ALA LEU LEU GLY ASN ARG SER TRP GLN THR ARG SEQRES 20 B 332 ALA LEU LEU ILE LYS ALA LEU ILE ASP GLN GLY TYR MET SEQRES 21 B 332 LYS GLN ILE LEU VAL SER ASN ASP TRP LEU PHE GLY PHE SEQRES 22 B 332 SER SER TYR VAL THR ASN ILE MET ASP VAL MET ASP SER SEQRES 23 B 332 VAL ASN PRO ASP GLY MET ALA PHE ILE PRO LEU ARG VAL SEQRES 24 B 332 ILE PRO PHE LEU ARG GLU LYS GLY VAL SER GLN GLU THR SEQRES 25 B 332 LEU ALA GLY ILE THR VAL THR ASN PRO ALA ARG PHE LEU SEQRES 26 B 332 SER PRO THR LEU ARG ALA SER HET FMT A 401 3 HET ZN A 402 1 HET ZN A 403 1 HET TA8 A 404 10 HET ZN B 401 1 HET FMT B 402 3 HET ZN B 403 1 HET ZN B 404 1 HET TA8 B 405 10 HETNAM FMT FORMIC ACID HETNAM ZN ZINC ION HETNAM TA8 POLYACRYLIC ACID HETSYN TA8 OCTANE-1,3,5,7-TETRACARBOXYLIC ACID FORMUL 3 FMT 2(C H2 O2) FORMUL 4 ZN 5(ZN 2+) FORMUL 6 TA8 2(C12 H18 O8) FORMUL 12 HOH *290(H2 O) HELIX 1 AA1 SER A 47 ALA A 49 5 3 HELIX 2 AA2 GLY A 64 TRP A 69 1 6 HELIX 3 AA3 PRO A 70 GLY A 74 5 5 HELIX 4 AA4 SER A 75 ALA A 93 1 19 HELIX 5 AA5 THR A 103 GLY A 107 5 5 HELIX 6 AA6 ASP A 109 ASP A 121 1 13 HELIX 7 AA7 PRO A 135 LEU A 140 1 6 HELIX 8 AA8 SER A 142 TYR A 156 1 15 HELIX 9 AA9 THR A 177 GLY A 195 1 19 HELIX 10 AB1 ALA A 203 GLN A 206 5 4 HELIX 11 AB2 ARG A 207 GLU A 219 1 13 HELIX 12 AB3 SER A 222 SER A 224 5 3 HELIX 13 AB4 HIS A 230 THR A 234 5 5 HELIX 14 AB5 ASP A 236 ARG A 246 1 11 HELIX 15 AB6 ASN A 265 GLY A 273 1 9 HELIX 16 AB7 SER A 276 GLN A 290 1 15 HELIX 17 AB8 TYR A 292 LYS A 294 5 3 HELIX 18 AB9 ASN A 312 ASN A 321 1 10 HELIX 19 AC1 ASP A 323 MET A 325 5 3 HELIX 20 AC2 ALA A 326 LYS A 339 1 14 HELIX 21 AC3 SER A 342 VAL A 351 1 10 HELIX 22 AC4 VAL A 351 SER A 359 1 9 HELIX 23 AC5 THR B 45 GLY B 50 1 6 HELIX 24 AC6 GLY B 64 TRP B 69 1 6 HELIX 25 AC7 PRO B 70 GLY B 74 5 5 HELIX 26 AC8 SER B 75 ALA B 93 1 19 HELIX 27 AC9 THR B 103 GLY B 107 5 5 HELIX 28 AD1 ASP B 109 ASP B 121 1 13 HELIX 29 AD2 PRO B 135 LEU B 140 1 6 HELIX 30 AD3 SER B 142 TYR B 156 1 15 HELIX 31 AD4 THR B 177 GLY B 195 1 19 HELIX 32 AD5 ALA B 203 GLN B 206 5 4 HELIX 33 AD6 ARG B 207 GLU B 219 1 13 HELIX 34 AD7 SER B 222 SER B 224 5 3 HELIX 35 AD8 HIS B 230 THR B 234 5 5 HELIX 36 AD9 ASP B 236 ARG B 246 1 11 HELIX 37 AE1 ASN B 265 GLY B 273 1 9 HELIX 38 AE2 SER B 276 GLN B 290 1 15 HELIX 39 AE3 TYR B 292 LYS B 294 5 3 HELIX 40 AE4 ASN B 312 ASN B 321 1 10 HELIX 41 AE5 ASP B 323 MET B 325 5 3 HELIX 42 AE6 ALA B 326 LYS B 339 1 14 HELIX 43 AE7 SER B 342 VAL B 351 1 10 HELIX 44 AE8 VAL B 351 SER B 359 1 9 SHEET 1 AA1 2 ARG A 36 THR A 39 0 SHEET 2 AA1 2 GLY A 42 THR A 45 -1 O ILE A 44 N ILE A 37 SHEET 1 AA2 3 THR A 52 GLU A 56 0 SHEET 2 AA2 3 THR A 97 ASP A 100 1 O VAL A 99 N LEU A 53 SHEET 3 AA2 3 HIS A 123 VAL A 125 1 O HIS A 123 N ILE A 98 SHEET 1 AA3 2 CYS A 59 GLY A 60 0 SHEET 2 AA3 2 GLY A 305 PHE A 306 1 O GLY A 305 N GLY A 60 SHEET 1 AA4 6 ALA A 127 GLY A 129 0 SHEET 2 AA4 6 ILE A 167 ALA A 171 1 O LYS A 169 N THR A 128 SHEET 3 AA4 6 VAL A 198 HIS A 201 1 O THR A 199 N ILE A 168 SHEET 4 AA4 6 VAL A 226 ILE A 228 1 O CYS A 227 N THR A 200 SHEET 5 AA4 6 LEU A 249 LEU A 252 1 O LEU A 249 N ILE A 228 SHEET 6 AA4 6 ILE A 296 VAL A 298 1 O LEU A 297 N LEU A 252 SHEET 1 AA5 2 ILE B 37 THR B 39 0 SHEET 2 AA5 2 GLY B 42 ILE B 44 -1 O ILE B 44 N ILE B 37 SHEET 1 AA6 8 THR B 52 GLU B 56 0 SHEET 2 AA6 8 THR B 97 ASP B 100 1 O VAL B 99 N LEU B 53 SHEET 3 AA6 8 HIS B 123 GLY B 129 1 O VAL B 125 N ASP B 100 SHEET 4 AA6 8 ILE B 167 ALA B 171 1 O LYS B 169 N THR B 128 SHEET 5 AA6 8 VAL B 198 HIS B 201 1 O THR B 199 N ILE B 168 SHEET 6 AA6 8 VAL B 226 ILE B 228 1 O CYS B 227 N VAL B 198 SHEET 7 AA6 8 LEU B 249 LEU B 252 1 O LEU B 249 N ILE B 228 SHEET 8 AA6 8 ILE B 296 VAL B 298 1 O LEU B 297 N LEU B 252 SHEET 1 AA7 2 CYS B 59 GLY B 60 0 SHEET 2 AA7 2 GLY B 305 PHE B 306 1 O GLY B 305 N GLY B 60 LINK NZ LYS A 169 C FMT A 401 1555 1555 1.32 LINK NZ LYS B 169 C FMT B 402 1555 1555 1.31 LINK NE2 HIS A 55 ZN ZN A 402 1555 1555 2.03 LINK NE2 HIS A 57 ZN ZN A 402 1555 1555 2.08 LINK ND1 HIS A 201 ZN ZN A 403 1555 1555 2.04 LINK NE2 HIS A 230 ZN ZN A 403 1555 1555 2.04 LINK OD1 ASP A 301 ZN ZN A 402 1555 1555 2.06 LINK O1 FMT A 401 ZN ZN A 402 1555 1555 2.08 LINK O2 FMT A 401 ZN ZN A 403 1555 1555 2.00 LINK ZN ZN A 402 O41 TA8 A 404 1555 1555 1.98 LINK ZN ZN A 403 O42 TA8 A 404 1555 1555 1.98 LINK ZN ZN A 403 O41 TA8 A 404 1555 1555 2.59 LINK NE2 HIS B 55 ZN ZN B 403 1555 1555 2.08 LINK NE2 HIS B 57 ZN ZN B 403 1555 1555 2.04 LINK ND1 HIS B 201 ZN ZN B 404 1555 1555 2.10 LINK NE2 HIS B 230 ZN ZN B 404 1555 1555 2.00 LINK OD1 ASP B 301 ZN ZN B 403 1555 1555 2.18 LINK O1 FMT B 402 ZN ZN B 403 1555 1555 2.08 LINK O2 FMT B 402 ZN ZN B 404 1555 1555 2.01 LINK ZN ZN B 403 O42 TA8 B 405 1555 1555 1.99 LINK ZN ZN B 404 O41 TA8 B 405 1555 1555 2.00 LINK ZN ZN B 404 O42 TA8 B 405 1555 1555 2.60 SITE 1 AC1 9 HIS A 55 HIS A 57 VAL A 101 LYS A 169 SITE 2 AC1 9 HIS A 201 HIS A 230 ZN A 402 ZN A 403 SITE 3 AC1 9 TA8 A 404 SITE 1 AC2 5 HIS A 55 HIS A 57 ASP A 301 FMT A 401 SITE 2 AC2 5 TA8 A 404 SITE 1 AC3 4 HIS A 201 HIS A 230 FMT A 401 TA8 A 404 SITE 1 AC4 10 HIS A 55 HIS A 57 TRP A 131 HIS A 201 SITE 2 AC4 10 HIS A 230 ASP A 301 FMT A 401 ZN A 402 SITE 3 AC4 10 ZN A 403 HOH A 501 SITE 1 AC5 2 SER B 342 THR B 345 SITE 1 AC6 5 HIS B 55 HIS B 57 ASP B 301 FMT B 402 SITE 2 AC6 5 TA8 B 405 SITE 1 AC7 4 HIS B 201 HIS B 230 FMT B 402 TA8 B 405 SITE 1 AC8 9 HIS B 55 HIS B 57 TRP B 131 HIS B 201 SITE 2 AC8 9 HIS B 230 ASP B 301 FMT B 402 ZN B 403 SITE 3 AC8 9 ZN B 404 SITE 1 AC9 15 HIS B 55 HIS B 57 VAL B 101 THR B 103 SITE 2 AC9 15 THR B 128 GLY B 129 LEU B 130 ILE B 168 SITE 3 AC9 15 VAL B 170 THR B 199 HIS B 201 HIS B 230 SITE 4 AC9 15 ZN B 403 ZN B 404 TA8 B 405 CRYST1 54.660 81.160 70.660 90.00 94.83 90.00 P 1 21 1 4 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.018295 0.000000 0.001546 0.00000 SCALE2 0.000000 0.012321 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014203 0.00000