HEADER TRANSFERASE 23-MAY-17 5VXE TITLE CRYSTAL STRUCTURE OF XANTHOMONAS CAMPESTRIS OLEA E117A BOUND WITH TITLE 2 CERULENIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: 3-OXOACYL-[ACP] SYNTHASE III; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: XANTHOMONAS CAMPESTRIS PV. CAMPESTRIS (STRAIN SOURCE 3 ATCC 33913 / DSM 3586 / NCPPB 528 / LMG 568 / P 25); SOURCE 4 ORGANISM_TAXID: 190485; SOURCE 5 STRAIN: ATCC 33913 / DSM 3586 / NCPPB 528 / LMG 568 / P 25; SOURCE 6 ATCC: 33913; SOURCE 7 GENE: FABH, XCC0212; SOURCE 8 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 9 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 10 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 11 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 12 EXPRESSION_SYSTEM_PLASMID: PET28B+ KEYWDS THIOLASE, TRANSFERASE, CONDENSATION EXPDTA X-RAY DIFFRACTION AUTHOR M.R.JENSEN,C.M.WILMOT REVDAT 4 04-OCT-23 5VXE 1 LINK REVDAT 3 01-JAN-20 5VXE 1 REMARK REVDAT 2 22-NOV-17 5VXE 1 JRNL REVDAT 1 25-OCT-17 5VXE 0 JRNL AUTH M.R.JENSEN,B.R.GOBLIRSCH,J.K.CHRISTENSON,M.A.ESLER, JRNL AUTH 2 F.A.MOHAMED,L.P.WACKETT,C.M.WILMOT JRNL TITL OLEA GLU117 IS KEY TO CONDENSATION OF TWO FATTY-ACYL JRNL TITL 2 COENZYME A SUBSTRATES IN LONG-CHAIN OLEFIN BIOSYNTHESIS. JRNL REF BIOCHEM. J. V. 474 3871 2017 JRNL REFN ESSN 1470-8728 JRNL PMID 29025976 JRNL DOI 10.1042/BCJ20170642 REMARK 2 REMARK 2 RESOLUTION. 1.66 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0158 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) : 1.66 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 3 NUMBER OF REFLECTIONS : 36667 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 : 0.210 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1925 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) : 1.66 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.70 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2599 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 97.10 REMARK 3 BIN R VALUE (WORKING SET) : 0.2440 REMARK 3 BIN FREE R VALUE SET COUNT : 144 REMARK 3 BIN FREE R VALUE : 0.2800 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2517 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 23 REMARK 3 SOLVENT ATOMS : 109 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 21.70 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 34.30 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.06000 REMARK 3 B22 (A**2) : -0.06000 REMARK 3 B33 (A**2) : 0.20000 REMARK 3 B12 (A**2) : -0.03000 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): 0.095 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.096 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.073 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 4.450 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.968 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.953 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2643 ; 0.031 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 2534 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3585 ; 2.757 ; 1.967 REMARK 3 BOND ANGLES OTHERS (DEGREES): 5861 ; 1.290 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 345 ; 6.988 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 109 ;33.314 ;24.220 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 456 ;16.445 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 18 ;22.366 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 420 ; 0.164 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2979 ; 0.014 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 522 ; 0.003 ; 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): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL 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 : 1 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 14 A 358 REMARK 3 ORIGIN FOR THE GROUP (A): 20.6023 -36.8730 8.0781 REMARK 3 T TENSOR REMARK 3 T11: 0.0144 T22: 0.1446 REMARK 3 T33: 0.0379 T12: 0.0168 REMARK 3 T13: 0.0024 T23: 0.0279 REMARK 3 L TENSOR REMARK 3 L11: 1.9842 L22: 0.5810 REMARK 3 L33: 0.6812 L12: 0.1067 REMARK 3 L13: -0.9376 L23: -0.2810 REMARK 3 S TENSOR REMARK 3 S11: 0.1230 S12: 0.4572 S13: 0.1126 REMARK 3 S21: -0.0167 S22: -0.0079 S23: 0.0252 REMARK 3 S31: -0.0483 S32: -0.2127 S33: -0.1151 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 5VXE COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 24-MAY-17. REMARK 100 THE DEPOSITION ID IS D_1000228023. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-JUN-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 23-ID-B REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.03317 REMARK 200 MONOCHROMATOR : SI 111 CHANNEL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MAR SCANNER 300 MM PLATE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 V705 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 V705, HKL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 38595 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.660 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 200 DATA REDUNDANCY : 5.600 REMARK 200 R MERGE (I) : 0.07700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.66 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.69 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.0 REMARK 200 DATA REDUNDANCY IN SHELL : 5.60 REMARK 200 R MERGE FOR SHELL (I) : 0.86500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.070 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER 5.8.0158 REMARK 200 STARTING MODEL: 3S21 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 41.31 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.26 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 13% PEG 4000, 100 MM MANGANESE REMARK 280 CHLORIDE, 100 MM MES PH 6.0, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 292K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 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+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+1/3 REMARK 290 6555 -X,-X+Y,-Z+2/3 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 46.38467 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 23.19233 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 23.19233 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 46.38467 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: 5840 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 26530 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -12.0 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 46.38467 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 MET A 1 REMARK 465 GLY A 2 REMARK 465 SER A 3 REMARK 465 SER A 4 REMARK 465 HIS A 5 REMARK 465 HIS A 6 REMARK 465 HIS A 7 REMARK 465 HIS A 8 REMARK 465 HIS A 9 REMARK 465 HIS A 10 REMARK 465 SER A 11 REMARK 465 SER A 12 REMARK 465 GLY A 13 REMARK 465 PRO A 187 REMARK 465 ASP A 188 REMARK 465 VAL A 189 REMARK 465 CYS A 239 REMARK 465 ARG A 240 REMARK 465 GLY A 241 REMARK 465 ASN A 242 REMARK 465 LEU A 243 REMARK 465 ASP A 244 REMARK 465 ARG A 245 REMARK 465 MET A 246 REMARK 465 VAL A 247 REMARK 465 THR A 248 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 OD1 ASP A 151 OH TYR A 224 1.90 REMARK 500 OD2 ASP A 151 NH2 ARG A 155 1.98 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 44 CD GLU A 44 OE2 0.090 REMARK 500 TYR A 53 CB TYR A 53 CG 0.091 REMARK 500 GLU A 101 CD GLU A 101 OE1 0.083 REMARK 500 TYR A 224 CG TYR A 224 CD2 -0.085 REMARK 500 TYR A 224 CE1 TYR A 224 CZ -0.130 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 55 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 ARG A 73 NE - CZ - NH1 ANGL. DEV. = 4.8 DEGREES REMARK 500 ASP A 78 CB - CG - OD1 ANGL. DEV. = 6.1 DEGREES REMARK 500 ASP A 83 CB - CG - OD2 ANGL. DEV. = -8.0 DEGREES REMARK 500 ARG A 90 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 ARG A 90 NE - CZ - NH2 ANGL. DEV. = -6.8 DEGREES REMARK 500 ASP A 151 CB - CG - OD1 ANGL. DEV. = 10.1 DEGREES REMARK 500 ASP A 151 CB - CG - OD2 ANGL. DEV. = -13.2 DEGREES REMARK 500 GLU A 158 OE1 - CD - OE2 ANGL. DEV. = -8.2 DEGREES REMARK 500 ARG A 159 NE - CZ - NH1 ANGL. DEV. = -4.0 DEGREES REMARK 500 ARG A 159 NE - CZ - NH2 ANGL. DEV. = 3.5 DEGREES REMARK 500 ASP A 163 CB - CG - OD1 ANGL. DEV. = 9.0 DEGREES REMARK 500 TYR A 164 CB - CG - CD1 ANGL. DEV. = -4.8 DEGREES REMARK 500 ARG A 183 NE - CZ - NH1 ANGL. DEV. = 4.2 DEGREES REMARK 500 ARG A 195 NE - CZ - NH1 ANGL. DEV. = 3.9 DEGREES REMARK 500 ARG A 195 NE - CZ - NH2 ANGL. DEV. = -3.5 DEGREES REMARK 500 ARG A 214 NE - CZ - NH1 ANGL. DEV. = 5.6 DEGREES REMARK 500 ARG A 214 NE - CZ - NH2 ANGL. DEV. = -3.6 DEGREES REMARK 500 ASP A 220 CB - CG - OD2 ANGL. DEV. = -6.8 DEGREES REMARK 500 TYR A 224 CB - CG - CD1 ANGL. DEV. = -4.5 DEGREES REMARK 500 TYR A 224 CZ - CE2 - CD2 ANGL. DEV. = -5.8 DEGREES REMARK 500 LYS A 225 CD - CE - NZ ANGL. DEV. = -16.0 DEGREES REMARK 500 ARG A 230 NE - CZ - NH1 ANGL. DEV. = 4.3 DEGREES REMARK 500 ASP A 280 CB - CG - OD1 ANGL. DEV. = -5.7 DEGREES REMARK 500 ASP A 280 CB - CG - OD2 ANGL. DEV. = 8.9 DEGREES REMARK 500 ASP A 302 CB - CG - OD1 ANGL. DEV. = 5.9 DEGREES REMARK 500 LEU A 334 CB - CG - CD1 ANGL. DEV. = 10.9 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 ASN A 25 37.42 -145.73 REMARK 500 VAL A 66 -61.21 -106.06 REMARK 500 ASN A 141 52.04 -164.03 REMARK 500 ALA A 142 -132.95 51.24 REMARK 500 ALA A 142 -135.12 51.24 REMARK 500 ASP A 169 114.48 -160.38 REMARK 500 MET A 184 50.37 -112.17 REMARK 500 THR A 250 -31.80 -140.64 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 MN A 403 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 38 ND1 REMARK 620 2 ASP A 76 OD1 83.5 REMARK 620 3 HOH A 508 O 97.0 179.4 REMARK 620 4 HOH A 516 O 168.0 103.9 75.6 REMARK 620 5 HOH A 518 O 106.9 93.1 86.5 82.4 REMARK 620 6 HOH A 554 O 97.7 86.1 94.0 73.8 155.2 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CER A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MN A 403 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5VXI RELATED DB: PDB REMARK 900 RELATED ID: 5VXD RELATED DB: PDB REMARK 900 RELATED ID: 5VXF RELATED DB: PDB REMARK 900 RELATED ID: 5VXH RELATED DB: PDB REMARK 900 RELATED ID: 5VXG RELATED DB: PDB DBREF 5VXE A 21 358 UNP Q8PDX2 Q8PDX2_XANCP 1 338 SEQADV 5VXE MET A 1 UNP Q8PDX2 INITIATING METHIONINE SEQADV 5VXE GLY A 2 UNP Q8PDX2 EXPRESSION TAG SEQADV 5VXE SER A 3 UNP Q8PDX2 EXPRESSION TAG SEQADV 5VXE SER A 4 UNP Q8PDX2 EXPRESSION TAG SEQADV 5VXE HIS A 5 UNP Q8PDX2 EXPRESSION TAG SEQADV 5VXE HIS A 6 UNP Q8PDX2 EXPRESSION TAG SEQADV 5VXE HIS A 7 UNP Q8PDX2 EXPRESSION TAG SEQADV 5VXE HIS A 8 UNP Q8PDX2 EXPRESSION TAG SEQADV 5VXE HIS A 9 UNP Q8PDX2 EXPRESSION TAG SEQADV 5VXE HIS A 10 UNP Q8PDX2 EXPRESSION TAG SEQADV 5VXE SER A 11 UNP Q8PDX2 EXPRESSION TAG SEQADV 5VXE SER A 12 UNP Q8PDX2 EXPRESSION TAG SEQADV 5VXE GLY A 13 UNP Q8PDX2 EXPRESSION TAG SEQADV 5VXE LEU A 14 UNP Q8PDX2 EXPRESSION TAG SEQADV 5VXE VAL A 15 UNP Q8PDX2 EXPRESSION TAG SEQADV 5VXE PRO A 16 UNP Q8PDX2 EXPRESSION TAG SEQADV 5VXE ARG A 17 UNP Q8PDX2 EXPRESSION TAG SEQADV 5VXE GLY A 18 UNP Q8PDX2 EXPRESSION TAG SEQADV 5VXE SER A 19 UNP Q8PDX2 EXPRESSION TAG SEQADV 5VXE HIS A 20 UNP Q8PDX2 EXPRESSION TAG SEQADV 5VXE ALA A 117 UNP Q8PDX2 GLU 97 ENGINEERED MUTATION SEQRES 1 A 358 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 A 358 LEU VAL PRO ARG GLY SER HIS MET LEU PHE GLN ASN VAL SEQRES 3 A 358 SER ILE ALA GLY LEU ALA HIS ILE ASP ALA PRO HIS THR SEQRES 4 A 358 LEU THR SER LYS GLU ILE ASN GLU ARG LEU GLN PRO THR SEQRES 5 A 358 TYR ASP ARG LEU GLY ILE LYS THR ASP VAL LEU GLY ASP SEQRES 6 A 358 VAL ALA GLY ILE HIS ALA ARG ARG LEU TRP ASP GLN ASP SEQRES 7 A 358 VAL GLN ALA SER ASP ALA ALA THR GLN ALA ALA ARG LYS SEQRES 8 A 358 ALA LEU ILE ASP ALA ASN ILE GLY ILE GLU LYS ILE GLY SEQRES 9 A 358 LEU LEU ILE ASN THR SER VAL SER ARG ASP TYR LEU ALA SEQRES 10 A 358 PRO SER THR ALA SER ILE VAL SER GLY ASN LEU GLY VAL SEQRES 11 A 358 SER ASP HIS CYS MET THR PHE ASP VAL ALA ASN ALA CYS SEQRES 12 A 358 LEU ALA PHE ILE ASN GLY MET ASP ILE ALA ALA ARG MET SEQRES 13 A 358 LEU GLU ARG GLY GLU ILE ASP TYR ALA LEU VAL VAL ASP SEQRES 14 A 358 GLY GLU THR ALA ASN LEU VAL TYR GLU LYS THR LEU GLU SEQRES 15 A 358 ARG MET THR SER PRO ASP VAL THR GLU GLU GLU PHE ARG SEQRES 16 A 358 ASN GLU LEU ALA ALA LEU THR LEU GLY CYS GLY ALA ALA SEQRES 17 A 358 ALA MET VAL MET ALA ARG SER GLU LEU VAL PRO ASP ALA SEQRES 18 A 358 PRO ARG TYR LYS GLY GLY VAL THR ARG SER ALA THR GLU SEQRES 19 A 358 TRP ASN LYS LEU CYS ARG GLY ASN LEU ASP ARG MET VAL SEQRES 20 A 358 THR ASP THR ARG LEU LEU LEU ILE GLU GLY ILE LYS LEU SEQRES 21 A 358 ALA GLN LYS THR PHE VAL ALA ALA LYS GLN VAL LEU GLY SEQRES 22 A 358 TRP ALA VAL GLU GLU LEU ASP GLN PHE VAL ILE HIS GLN SEQRES 23 A 358 VAL SER ARG PRO HIS THR ALA ALA PHE VAL LYS SER PHE SEQRES 24 A 358 GLY ILE ASP PRO ALA LYS VAL MET THR ILE PHE GLY GLU SEQRES 25 A 358 HIS GLY ASN ILE GLY PRO ALA SER VAL PRO ILE VAL LEU SEQRES 26 A 358 SER LYS LEU LYS GLU LEU GLY ARG LEU LYS LYS GLY ASP SEQRES 27 A 358 ARG ILE ALA LEU LEU GLY ILE GLY SER GLY LEU ASN CYS SEQRES 28 A 358 SER MET ALA GLU VAL VAL TRP HET CER A 401 16 HET GOL A 402 6 HET MN A 403 1 HETNAM CER (2S, 3R)-3-HYDROXY-4-OXO-7,10-TRANS,TRANS- HETNAM 2 CER DODECADIENAMIDE HETNAM GOL GLYCEROL HETNAM MN MANGANESE (II) ION HETSYN CER CERULENIN HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 CER C12 H19 N O3 FORMUL 3 GOL C3 H8 O3 FORMUL 4 MN MN 2+ FORMUL 5 HOH *109(H2 O) HELIX 1 AA1 ARG A 17 LEU A 22 5 6 HELIX 2 AA2 SER A 42 GLY A 57 1 16 HELIX 3 AA3 ASP A 61 VAL A 66 1 6 HELIX 4 AA4 GLN A 80 ASN A 97 1 18 HELIX 5 AA5 GLY A 99 ILE A 103 5 5 HELIX 6 AA6 SER A 119 GLY A 129 1 11 HELIX 7 AA7 ASN A 141 CYS A 143 5 3 HELIX 8 AA8 LEU A 144 ARG A 159 1 16 HELIX 9 AA9 ALA A 173 MET A 184 1 12 HELIX 10 AB1 GLU A 191 ALA A 199 1 9 HELIX 11 AB2 ALA A 200 LEU A 203 5 4 HELIX 12 AB3 GLU A 216 VAL A 218 5 3 HELIX 13 AB4 THR A 233 ASN A 236 5 4 HELIX 14 AB5 THR A 250 GLY A 273 1 24 HELIX 15 AB6 ALA A 275 LEU A 279 5 5 HELIX 16 AB7 SER A 288 GLY A 300 1 13 HELIX 17 AB8 ASP A 302 VAL A 306 5 5 HELIX 18 AB9 ILE A 309 GLY A 314 1 6 HELIX 19 AC1 ILE A 316 PRO A 318 5 3 HELIX 20 AC2 ALA A 319 LEU A 331 1 13 SHEET 1 AA1 5 VAL A 26 ASP A 35 0 SHEET 2 AA1 5 GLY A 206 ARG A 214 -1 O VAL A 211 N GLY A 30 SHEET 3 AA1 5 TYR A 164 GLU A 171 -1 N VAL A 167 O MET A 210 SHEET 4 AA1 5 LEU A 105 ASN A 108 1 N LEU A 105 O LEU A 166 SHEET 5 AA1 5 MET A 135 ASP A 138 1 O MET A 135 N LEU A 106 SHEET 1 AA2 2 HIS A 38 THR A 41 0 SHEET 2 AA2 2 ALA A 71 LEU A 74 -1 O LEU A 74 N HIS A 38 SHEET 1 AA3 4 ARG A 223 SER A 231 0 SHEET 2 AA3 4 ASN A 350 VAL A 357 -1 O VAL A 357 N ARG A 223 SHEET 3 AA3 4 ARG A 339 GLY A 346 -1 N LEU A 342 O ALA A 354 SHEET 4 AA3 4 GLN A 281 ILE A 284 1 N VAL A 283 O ALA A 341 LINK ND1 HIS A 38 MN MN A 403 1555 1555 2.39 LINK OD1 ASP A 76 MN MN A 403 1555 1555 2.29 LINK MN MN A 403 O HOH A 508 1555 2444 2.20 LINK MN MN A 403 O HOH A 516 1555 2444 2.26 LINK MN MN A 403 O HOH A 518 1555 1555 2.08 LINK MN MN A 403 O HOH A 554 1555 2444 2.35 CISPEP 1 ALA A 117 PRO A 118 0 -2.73 CISPEP 2 GLY A 348 LEU A 349 0 -12.94 SITE 1 AC1 10 ALA A 142 CYS A 143 LEU A 253 HIS A 285 SITE 2 AC1 10 VAL A 287 HIS A 291 ASN A 315 ILE A 345 SITE 3 AC1 10 GLY A 346 SER A 347 SITE 1 AC2 7 GLN A 87 ASP A 132 HIS A 133 ARG A 230 SITE 2 AC2 7 LYS A 263 GLN A 270 HOH A 591 SITE 1 AC3 6 HIS A 38 ASP A 76 HOH A 508 HOH A 516 SITE 2 AC3 6 HOH A 518 HOH A 554 CRYST1 89.965 89.965 69.577 90.00 90.00 120.00 P 32 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 0.011115 0.006417 0.000000 0.00000 SCALE2 0.000000 0.012835 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014373 0.00000