HEADER HYDROLASE 22-MAR-18 6G23 OBSLTE 25-OCT-23 6G23 8P7U TITLE PHOSPHOTRIESTERASE PTE_C23M_2 COMPND MOL_ID: 1; COMPND 2 MOLECULE: PARATHION HYDROLASE; COMPND 3 CHAIN: A; 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 3 14-FEB-24 6G23 1 REMARK REVDAT 2 25-OCT-23 6G23 1 OBSLTE LINK REVDAT 1 10-APR-19 6G23 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_C23M_2 JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.38 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 : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.38 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 18.11 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 3 NUMBER OF REFLECTIONS : 90863 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) : 0.159 REMARK 3 R VALUE (WORKING SET) : 0.158 REMARK 3 FREE R VALUE : 0.177 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 4684 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) : 1.38 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.41 REMARK 3 REFLECTION IN BIN (WORKING SET) : 6542 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.64 REMARK 3 BIN R VALUE (WORKING SET) : 0.2670 REMARK 3 BIN FREE R VALUE SET COUNT : 329 REMARK 3 BIN FREE R VALUE : 0.2710 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2498 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 39 REMARK 3 SOLVENT ATOMS : 356 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 17.91 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.15000 REMARK 3 B22 (A**2) : 0.15000 REMARK 3 B33 (A**2) : -0.31000 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): 0.042 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.044 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.029 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 0.741 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.974 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.968 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2616 ; 0.032 ; 0.020 REMARK 3 BOND LENGTHS OTHERS (A): 2483 ; 0.003 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3549 ; 2.678 ; 1.970 REMARK 3 BOND ANGLES OTHERS (DEGREES): 5705 ; 1.275 ; 3.004 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 337 ; 6.548 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 106 ;33.756 ;22.170 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 417 ;11.584 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 27 ;16.860 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 415 ; 0.159 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2928 ; 0.014 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 560 ; 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): 1337 ; 1.601 ; 1.557 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1338 ; 1.601 ; 1.557 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1677 ; 2.297 ; 2.332 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 1678 ; 2.307 ; 2.334 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1279 ; 3.104 ; 1.818 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1280 ; 3.103 ; 1.818 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 1873 ; 4.229 ; 2.638 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 3105 ; 5.325 ;20.789 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 3006 ; 5.149 ;20.035 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 6G23 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 22-MAR-18. REMARK 100 THE DEPOSITION ID IS D_1200009301. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-JAN-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID23-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.27242 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M-F REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 95348 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.380 REMARK 200 RESOLUTION RANGE LOW (A) : 18.110 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 200 DATA REDUNDANCY : 6.500 REMARK 200 R MERGE (I) : 0.05112 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 6.9100 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.38 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.43 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.8 REMARK 200 DATA REDUNDANCY IN SHELL : 6.10 REMARK 200 R MERGE FOR SHELL (I) : 0.26850 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.080 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 (%): 61.19 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.17 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M TRIS PH=8 1.5M (NH4)2SO4 12% REMARK 280 GLYCEROL, PH 8, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 93.53500 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 34.84500 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 34.84500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 140.30250 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 34.84500 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 34.84500 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 46.76750 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 34.84500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 34.84500 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 140.30250 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 34.84500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 34.84500 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 46.76750 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 93.53500 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: 4550 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 22730 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -75.0 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 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 778 LIES ON A SPECIAL POSITION. REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 GLY A 34 REMARK 465 SER A 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 GLU A 263 CG CD OE1 OE2 REMARK 470 ASP A 264 CG OD1 OD2 REMARK 470 GLU A 338 CD OE1 OE2 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 C4 FU2 A 404 O HOH A 503 1.57 REMARK 500 OG1 THR A 345 CAE E8N A 408 1.59 REMARK 500 C4 FU2 A 404 O HOH A 502 1.63 REMARK 500 OG SER A 342 CAE E8N A 408 1.78 REMARK 500 O HOH A 548 O HOH A 627 1.89 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 TYR A 156 CE1 TYR A 156 CZ -0.106 REMARK 500 ARG A 225 CD ARG A 225 NE -0.116 REMARK 500 ARG A 225 CZ ARG A 225 NH1 -0.080 REMARK 500 ARG A 356 CZ ARG A 356 NH2 -0.083 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 67 NE - CZ - NH2 ANGL. DEV. = 3.2 DEGREES REMARK 500 ARG A 85 NE - CZ - NH1 ANGL. DEV. = 4.9 DEGREES REMARK 500 ARG A 85 NE - CZ - NH2 ANGL. DEV. = -5.3 DEGREES REMARK 500 ARG A 88 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 ARG A 89 NE - CZ - NH2 ANGL. DEV. = 4.3 DEGREES REMARK 500 ARG A 96 NE - CZ - NH1 ANGL. DEV. = 6.2 DEGREES REMARK 500 ASP A 109 CB - CG - OD2 ANGL. DEV. = -5.5 DEGREES REMARK 500 ARG A 118 NE - CZ - NH1 ANGL. DEV. = 4.1 DEGREES REMARK 500 ARG A 139 CG - CD - NE ANGL. DEV. = 19.3 DEGREES REMARK 500 ARG A 139 NE - CZ - NH1 ANGL. DEV. = 6.9 DEGREES REMARK 500 ARG A 152 NE - CZ - NH1 ANGL. DEV. = 7.9 DEGREES REMARK 500 ARG A 152 NE - CZ - NH2 ANGL. DEV. = -7.3 DEGREES REMARK 500 TYR A 156 CZ - CE2 - CD2 ANGL. DEV. = -6.1 DEGREES REMARK 500 ASP A 160 CB - CG - OD1 ANGL. DEV. = 6.2 DEGREES REMARK 500 ARG A 185 NE - CZ - NH1 ANGL. DEV. = -4.6 DEGREES REMARK 500 ARG A 207 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 ARG A 225 NE - CZ - NH1 ANGL. DEV. = 4.7 DEGREES REMARK 500 ASP A 233 CB - CG - OD1 ANGL. DEV. = 6.0 DEGREES REMARK 500 ASP A 235 CB - CG - OD2 ANGL. DEV. = -8.0 DEGREES REMARK 500 ASP A 236 CB - CG - OD1 ANGL. DEV. = 5.4 DEGREES REMARK 500 TYR A 248 CB - CG - CD2 ANGL. DEV. = 4.1 DEGREES REMARK 500 ARG A 275 NE - CZ - NH1 ANGL. DEV. = 4.4 DEGREES REMARK 500 ARG A 275 NE - CZ - NH2 ANGL. DEV. = -5.0 DEGREES REMARK 500 PHE A 306 CB - CG - CD1 ANGL. DEV. = 5.2 DEGREES REMARK 500 PHE A 327 CB - CG - CD2 ANGL. DEV. = -4.4 DEGREES REMARK 500 PHE A 327 CB - CG - CD1 ANGL. DEV. = 4.3 DEGREES REMARK 500 THR A 361 CB - CA - C ANGL. DEV. = -18.0 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 SER A 61 -143.79 -138.94 REMARK 500 TRP A 69 57.70 -142.42 REMARK 500 THR A 128 -167.84 -110.14 REMARK 500 TRP A 131 -154.41 -95.74 REMARK 500 GLU A 159 -133.92 54.07 REMARK 500 LEU A 252 79.98 -101.05 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 GLY A 261 LEU A 262 148.51 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 TYR A 248 0.07 SIDE CHAIN 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 ZN A 402 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 55 NE2 REMARK 620 2 HIS A 57 NE2 120.3 REMARK 620 3 ASP A 301 OD1 84.2 89.8 REMARK 620 4 FMT A 401 O2 96.9 89.1 178.7 REMARK 620 5 HOH A 502 O 112.0 126.7 85.9 94.3 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 99.5 REMARK 620 3 FMT A 401 O1 102.8 111.6 REMARK 620 4 HOH A 503 O 96.9 125.9 114.2 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 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 FU2 A 404 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 405 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 406 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 407 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue E8N A 408 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 409 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 6G1J RELATED DB: PDB DBREF 6G23 A 34 365 UNP P0A434 OPD_BREDI 34 365 SEQADV 6G23 ALA A 77 UNP P0A434 LYS 77 CONFLICT SEQADV 6G23 VAL A 80 UNP P0A434 ALA 80 CONFLICT SEQADV 6G23 GLU A 132 UNP P0A434 PHE 132 CONFLICT SEQADV 6G23 ASN A 173 UNP P0A434 THR 173 CONFLICT SEQADV 6G23 ARG A 185 UNP P0A434 LYS 185 CONFLICT SEQADV 6G23 LEU A 203 UNP P0A434 ALA 203 CONFLICT SEQADV 6G23 GLY A 254 UNP P0A434 HIS 254 CONFLICT SEQADV 6G23 ASN A 274 UNP P0A434 ILE 274 CONFLICT SEQADV 6G23 SER A 319 UNP P0A434 ARG 319 CONFLICT SEQADV 6G23 SER A 342 UNP P0A434 PRO 342 CONFLICT SEQADV 6G23 ASN A 343 UNP P0A434 GLN 343 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 LEU 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 ASN 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 HET FMT A 401 3 HET ZN A 402 1 HET ZN A 403 1 HET FU2 A 404 7 HET GOL A 405 6 HET GOL A 406 6 HET SO4 A 407 5 HET E8N A 408 9 HET ZN A 409 1 HETNAM FMT FORMIC ACID HETNAM ZN ZINC ION HETNAM FU2 FURFURAL HETNAM GOL GLYCEROL HETNAM SO4 SULFATE ION HETNAM E8N 1-ETHYL-1-METHYL-CYCLOHEXANE HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 FMT C H2 O2 FORMUL 3 ZN 3(ZN 2+) FORMUL 5 FU2 C5 H4 O2 FORMUL 6 GOL 2(C3 H8 O3) FORMUL 8 SO4 O4 S 2- FORMUL 9 E8N C9 H18 FORMUL 11 HOH *356(H2 O) HELIX 1 AA1 ILE A 46 GLY A 50 1 5 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 LEU 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 ARG A 331 1 6 HELIX 21 AC3 ARG A 331 LYS A 339 1 9 HELIX 22 AC4 SER A 342 VAL A 351 1 10 HELIX 23 AC5 VAL A 351 SER A 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 VAL A 125 N ASP A 100 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 VAL A 198 SHEET 5 AA4 6 LEU A 249 LEU A 252 1 O LEU A 249 N VAL A 226 SHEET 6 AA4 6 ILE A 296 VAL A 298 1 O LEU A 297 N LEU A 252 LINK NZ LYS A 169 C FMT A 401 1555 1555 1.39 LINK NE2 HIS A 55 ZN ZN A 402 1555 1555 2.05 LINK NE2 HIS A 57 ZN ZN A 402 1555 1555 2.03 LINK ND1 HIS A 201 ZN ZN A 403 1555 1555 2.05 LINK NE2 HIS A 230 ZN ZN A 403 1555 1555 1.99 LINK OD1 ASP A 301 ZN ZN A 402 1555 1555 2.26 LINK O2 FMT A 401 ZN ZN A 402 1555 1555 2.13 LINK O1 FMT A 401 ZN ZN A 403 1555 1555 1.91 LINK ZN ZN A 402 O HOH A 502 1555 1555 1.89 LINK ZN ZN A 403 O HOH A 503 1555 1555 1.98 SITE 1 AC1 10 HIS A 55 HIS A 57 TRP A 131 LYS A 169 SITE 2 AC1 10 HIS A 201 HIS A 230 ZN A 402 ZN A 403 SITE 3 AC1 10 FU2 A 404 HOH A 502 SITE 1 AC2 6 HIS A 55 HIS A 57 ASP A 301 FMT A 401 SITE 2 AC2 6 FU2 A 404 HOH A 502 SITE 1 AC3 6 HIS A 201 HIS A 230 FMT A 401 FU2 A 404 SITE 2 AC3 6 HOH A 502 HOH A 503 SITE 1 AC4 11 HIS A 57 ILE A 106 TRP A 131 ASP A 301 SITE 2 AC4 11 FMT A 401 ZN A 402 ZN A 403 HOH A 502 SITE 3 AC4 11 HOH A 503 HOH A 517 HOH A 730 SITE 1 AC5 10 TYR A 156 GLY A 157 ILE A 158 GLU A 159 SITE 2 AC5 10 ASP A 160 THR A 161 GLY A 162 HOH A 561 SITE 3 AC5 10 HOH A 583 HOH A 585 SITE 1 AC6 8 ALA A 63 GLY A 64 ARG A 67 GLY A 107 SITE 2 AC6 8 ARG A 108 GLU A 159 HOH A 542 HOH A 579 SITE 1 AC7 5 TRP A 277 GLN A 278 ARG A 331 HOH A 562 SITE 2 AC7 5 HOH A 688 SITE 1 AC8 6 GLU A 144 SER A 342 THR A 345 HOH A 750 SITE 2 AC8 6 HOH A 789 HOH A 854 SITE 1 AC9 3 LYS A 175 ALA A 176 PRO A 178 CRYST1 69.690 69.690 187.070 90.00 90.00 90.00 P 43 21 2 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 0.014349 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014349 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005346 0.00000