HEADER HYDROLASE 08-NOV-06 2E25 TITLE THE CRYSTAL STRUCTURE OF THE T109S MUTANT OF E. COLI DIHYDROOROTASE TITLE 2 COMPLEXED WITH AN INHIBITOR 5-FLUOROOROTATE COMPND MOL_ID: 1; COMPND 2 MOLECULE: DIHYDROOROTASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: DHOASE; COMPND 5 EC: 3.5.2.3; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562; SOURCE 4 GENE: PYRC; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: X7014A; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PBLUESCRIPT KEYWDS TIM BARREL, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR M.LEE,M.J.MAHER,J.M.GUSS REVDAT 7 15-NOV-23 2E25 1 REMARK REVDAT 6 25-OCT-23 2E25 1 REMARK REVDAT 5 10-NOV-21 2E25 1 REMARK SEQADV LINK REVDAT 4 13-JUL-11 2E25 1 VERSN REVDAT 3 24-FEB-09 2E25 1 VERSN REVDAT 2 22-MAY-07 2E25 1 HETATM REVDAT 1 13-MAR-07 2E25 0 JRNL AUTH M.LEE,M.J.MAHER,J.M.GUSS JRNL TITL STRUCTURE OF THE T109S MUTANT OF ESCHERICHIA COLI JRNL TITL 2 DIHYDROOROTASE COMPLEXED WITH THE INHIBITOR 5-FLUOROOROTATE: JRNL TITL 3 CATALYTIC ACTIVITY IS REFLECTED BY THE CRYSTAL FORM JRNL REF ACTA CRYSTALLOGR.,SECT.F V. 63 154 2007 JRNL REFN ESSN 1744-3091 JRNL PMID 17329804 JRNL DOI 10.1107/S1744309107004009 REMARK 2 REMARK 2 RESOLUTION. 2.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0005 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) : 2.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 75.8 REMARK 3 NUMBER OF REFLECTIONS : 10367 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) : 0.220 REMARK 3 R VALUE (WORKING SET) : 0.218 REMARK 3 FREE R VALUE : 0.257 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.700 REMARK 3 FREE R VALUE TEST SET COUNT : 490 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) : 2.70 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.77 REMARK 3 REFLECTION IN BIN (WORKING SET) : 281 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 29.92 REMARK 3 BIN R VALUE (WORKING SET) : 0.1870 REMARK 3 BIN FREE R VALUE SET COUNT : 8 REMARK 3 BIN FREE R VALUE : 0.2310 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2693 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 14 REMARK 3 SOLVENT ATOMS : 10 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : 73.80 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 63.00 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.29000 REMARK 3 B22 (A**2) : -0.29000 REMARK 3 B33 (A**2) : 0.59000 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): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.405 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.273 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 26.500 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.942 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.905 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2761 ; 0.006 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 2506 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3758 ; 0.932 ; 1.960 REMARK 3 BOND ANGLES OTHERS (DEGREES): 5803 ; 0.695 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 342 ; 5.346 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 130 ;33.841 ;23.462 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 443 ;12.952 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 22 ;16.401 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 425 ; 0.052 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3095 ; 0.002 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 567 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 579 ; 0.194 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 2667 ; 0.156 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1376 ; 0.166 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): 1592 ; 0.077 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 65 ; 0.133 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 1 ; 0.072 ; 0.200 REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 4 ; 0.057 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 32 ; 0.184 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 3 ; 0.131 ; 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): 2217 ; 2.307 ; 4.000 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 687 ; 0.434 ; 4.000 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2779 ; 3.055 ; 6.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1189 ; 1.887 ; 4.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 979 ; 2.919 ; 6.000 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 4 A 346 REMARK 3 ORIGIN FOR THE GROUP (A): 0.4207 23.4841 13.5678 REMARK 3 T TENSOR REMARK 3 T11: 0.1745 T22: 0.2625 REMARK 3 T33: -0.0401 T12: -0.3773 REMARK 3 T13: 0.0389 T23: 0.0126 REMARK 3 L TENSOR REMARK 3 L11: 2.9144 L22: 2.7729 REMARK 3 L33: 3.7470 L12: -1.0743 REMARK 3 L13: 0.0253 L23: 0.6586 REMARK 3 S TENSOR REMARK 3 S11: -0.2310 S12: -0.2755 S13: -0.1253 REMARK 3 S21: 0.2879 S22: 0.2376 S23: 0.0344 REMARK 3 S31: -0.4517 S32: -0.9982 S33: -0.0066 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 2E25 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 13-NOV-06. REMARK 100 THE DEPOSITION ID IS D_1000026131. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-APR-06 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.25 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) : 0.9793 REMARK 200 MONOCHROMATOR : GRAPHITE REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 300 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 16140 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 60.9 REMARK 200 DATA REDUNDANCY : 6.100 REMARK 200 R MERGE (I) : 0.04300 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 19.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.24 REMARK 200 COMPLETENESS FOR SHELL (%) : 38.2 REMARK 200 DATA REDUNDANCY IN SHELL : 3.40 REMARK 200 R MERGE FOR SHELL (I) : 0.20300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.100 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: PDB ENTRY 1XGE CHAIN A REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 58.91 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.99 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 14% PEG 3350, 0.1M MES, 75MM MGCL2, REMARK 280 0.15M KCL, PH 6.25, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 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+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 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 88.06000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 36.30500 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 36.30500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 44.03000 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 36.30500 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 36.30500 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 132.09000 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 36.30500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 36.30500 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 44.03000 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 36.30500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 36.30500 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 132.09000 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 88.06000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 300 REMARK: THE SECOND MONOMER OF THE BIOLOGICAL DIMER IS GENERATED BY REMARK 300 THE TWO FOLD AXIS: Y, Z, -X. 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 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 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 THR A 1 REMARK 465 ALA A 2 REMARK 465 PRO A 3 REMARK 465 GLN A 347 REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 ARG A 342 CG CD NE CZ NH1 NH2 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 HIS A 16 103.04 -165.58 REMARK 500 ARG A 20 -156.01 60.31 REMARK 500 ASN A 107 117.39 -167.93 REMARK 500 VAL A 160 -56.44 -137.34 REMARK 500 LEU A 168 79.71 -110.88 REMARK 500 HIS A 177 67.35 21.79 REMARK 500 VAL A 297 -53.64 -130.60 REMARK 500 ASP A 330 -162.39 68.72 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 CYS A 295 SER A 296 -138.59 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 401 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 16 NE2 REMARK 620 2 HIS A 18 NE2 127.7 REMARK 620 3 KCX A 102 OQ2 93.9 103.5 REMARK 620 4 ASP A 250 OD1 91.1 81.9 168.0 REMARK 620 5 HOH A 420 O 122.4 106.7 90.2 77.9 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 400 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 KCX A 102 OQ1 REMARK 620 2 HIS A 139 ND1 97.0 REMARK 620 3 HIS A 177 NE2 104.1 94.1 REMARK 620 4 FOT A 410 O6 119.8 79.7 136.1 REMARK 620 5 HOH A 420 O 114.4 136.0 106.4 58.4 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 ZN A 400 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FOT A 410 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1XGE RELATED DB: PDB REMARK 900 WILD-TYPE PROTEIN COMPLEXED WITH L-DHO DBREF 2E25 A 1 347 UNP P05020 PYRC_ECOLI 1 347 SEQADV 2E25 KCX A 102 UNP P05020 LYS 102 MODIFIED RESIDUE SEQADV 2E25 SER A 109 UNP P05020 THR 109 ENGINEERED MUTATION SEQADV 2E25 VAL A 119 UNP P05020 ILE 119 CONFLICT SEQRES 1 A 347 THR ALA PRO SER GLN VAL LEU LYS ILE ARG ARG PRO ASP SEQRES 2 A 347 ASP TRP HIS LEU HIS LEU ARG ASP GLY ASP MET LEU LYS SEQRES 3 A 347 THR VAL VAL PRO TYR THR SER GLU ILE TYR GLY ARG ALA SEQRES 4 A 347 ILE VAL MET PRO ASN LEU ALA PRO PRO VAL THR THR VAL SEQRES 5 A 347 GLU ALA ALA VAL ALA TYR ARG GLN ARG ILE LEU ASP ALA SEQRES 6 A 347 VAL PRO ALA GLY HIS ASP PHE THR PRO LEU MET THR CYS SEQRES 7 A 347 TYR LEU THR ASP SER LEU ASP PRO ASN GLU LEU GLU ARG SEQRES 8 A 347 GLY PHE ASN GLU GLY VAL PHE THR ALA ALA KCX LEU TYR SEQRES 9 A 347 PRO ALA ASN ALA SER THR ASN SER SER HIS GLY VAL THR SEQRES 10 A 347 SER VAL ASP ALA ILE MET PRO VAL LEU GLU ARG MET GLU SEQRES 11 A 347 LYS ILE GLY MET PRO LEU LEU VAL HIS GLY GLU VAL THR SEQRES 12 A 347 HIS ALA ASP ILE ASP ILE PHE ASP ARG GLU ALA ARG PHE SEQRES 13 A 347 ILE GLU SER VAL MET GLU PRO LEU ARG GLN ARG LEU THR SEQRES 14 A 347 ALA LEU LYS VAL VAL PHE GLU HIS ILE THR THR LYS ASP SEQRES 15 A 347 ALA ALA ASP TYR VAL ARG ASP GLY ASN GLU ARG LEU ALA SEQRES 16 A 347 ALA THR ILE THR PRO GLN HIS LEU MET PHE ASN ARG ASN SEQRES 17 A 347 HIS MET LEU VAL GLY GLY VAL ARG PRO HIS LEU TYR CYS SEQRES 18 A 347 LEU PRO ILE LEU LYS ARG ASN ILE HIS GLN GLN ALA LEU SEQRES 19 A 347 ARG GLU LEU VAL ALA SER GLY PHE ASN ARG VAL PHE LEU SEQRES 20 A 347 GLY THR ASP SER ALA PRO HIS ALA ARG HIS ARG LYS GLU SEQRES 21 A 347 SER SER CYS GLY CYS ALA GLY CYS PHE ASN ALA PRO THR SEQRES 22 A 347 ALA LEU GLY SER TYR ALA THR VAL PHE GLU GLU MET ASN SEQRES 23 A 347 ALA LEU GLN HIS PHE GLU ALA PHE CYS SER VAL ASN GLY SEQRES 24 A 347 PRO GLN PHE TYR GLY LEU PRO VAL ASN ASP THR PHE ILE SEQRES 25 A 347 GLU LEU VAL ARG GLU GLU GLN GLN VAL ALA GLU SER ILE SEQRES 26 A 347 ALA LEU THR ASP ASP THR LEU VAL PRO PHE LEU ALA GLY SEQRES 27 A 347 GLU THR VAL ARG TRP SER VAL LYS GLN MODRES 2E25 KCX A 102 LYS LYSINE NZ-CARBOXYLIC ACID HET KCX A 102 12 HET ZN A 400 1 HET ZN A 401 1 HET FOT A 410 12 HETNAM KCX LYSINE NZ-CARBOXYLIC ACID HETNAM ZN ZINC ION HETNAM FOT 5-FLUORO-2,6-DIOXO-1,2,3,6-TETRAHYDROPYRIMIDINE-4- HETNAM 2 FOT CARBOXYLIC ACID HETSYN FOT 5-FLUOROOROTIC ACID FORMUL 1 KCX C7 H14 N2 O4 FORMUL 2 ZN 2(ZN 2+) FORMUL 4 FOT C5 H3 F N2 O4 FORMUL 5 HOH *10(H2 O) HELIX 1 1 ASP A 21 GLU A 34 1 14 HELIX 2 2 THR A 51 VAL A 66 1 16 HELIX 3 3 ASP A 85 GLU A 95 1 11 HELIX 4 4 ILE A 122 ILE A 132 1 11 HELIX 5 5 ASP A 148 PHE A 150 5 3 HELIX 6 6 ASP A 151 VAL A 160 1 10 HELIX 7 7 VAL A 160 LEU A 168 1 9 HELIX 8 8 THR A 180 ASP A 189 1 10 HELIX 9 9 THR A 199 PHE A 205 1 7 HELIX 10 10 ASN A 206 VAL A 212 1 7 HELIX 11 11 ARG A 216 TYR A 220 5 5 HELIX 12 12 ARG A 227 GLY A 241 1 15 HELIX 13 13 ALA A 255 GLU A 260 1 6 HELIX 14 14 THR A 273 MET A 285 1 13 HELIX 15 15 ALA A 287 GLN A 289 5 3 HELIX 16 16 HIS A 290 VAL A 297 1 8 HELIX 17 17 VAL A 297 GLY A 304 1 8 SHEET 1 A 3 VAL A 6 ARG A 10 0 SHEET 2 A 3 PHE A 311 VAL A 315 -1 O LEU A 314 N LEU A 7 SHEET 3 A 3 SER A 344 VAL A 345 -1 O SER A 344 N VAL A 315 SHEET 1 B 8 ASP A 13 LEU A 17 0 SHEET 2 B 8 ARG A 38 VAL A 41 1 O ILE A 40 N ASP A 14 SHEET 3 B 8 THR A 73 TYR A 79 1 O LEU A 75 N ALA A 39 SHEET 4 B 8 PHE A 98 LEU A 103 1 O THR A 99 N MET A 76 SHEET 5 B 8 LEU A 136 VAL A 138 1 O LEU A 137 N ALA A 101 SHEET 6 B 8 VAL A 173 PHE A 175 1 O VAL A 174 N LEU A 136 SHEET 7 B 8 LEU A 194 ILE A 198 1 O ALA A 195 N PHE A 175 SHEET 8 B 8 VAL A 245 LEU A 247 1 O PHE A 246 N ALA A 196 SHEET 1 C 2 GLN A 319 GLN A 320 0 SHEET 2 C 2 THR A 340 VAL A 341 -1 O VAL A 341 N GLN A 319 SHEET 1 D 2 ILE A 325 ALA A 326 0 SHEET 2 D 2 THR A 331 LEU A 332 -1 O LEU A 332 N ILE A 325 LINK C ALA A 101 N KCX A 102 1555 1555 1.33 LINK C KCX A 102 N LEU A 103 1555 1555 1.33 LINK NE2 HIS A 16 ZN ZN A 401 1555 1555 2.19 LINK NE2 HIS A 18 ZN ZN A 401 1555 1555 2.10 LINK OQ1 KCX A 102 ZN ZN A 400 1555 1555 1.95 LINK OQ2 KCX A 102 ZN ZN A 401 1555 1555 2.23 LINK ND1 HIS A 139 ZN ZN A 400 1555 1555 2.19 LINK NE2 HIS A 177 ZN ZN A 400 1555 1555 2.08 LINK OD1 ASP A 250 ZN ZN A 401 1555 1555 2.27 LINK ZN ZN A 400 O6 FOT A 410 1555 1555 2.74 LINK ZN ZN A 400 O HOH A 420 1555 1555 2.25 LINK ZN ZN A 401 O HOH A 420 1555 1555 2.13 CISPEP 1 ALA A 46 PRO A 47 0 -0.71 CISPEP 2 LEU A 222 PRO A 223 0 7.40 SITE 1 AC1 6 KCX A 102 HIS A 139 HIS A 177 ZN A 401 SITE 2 AC1 6 FOT A 410 HOH A 420 SITE 1 AC2 6 HIS A 16 HIS A 18 KCX A 102 ASP A 250 SITE 2 AC2 6 ZN A 400 HOH A 420 SITE 1 AC3 12 HIS A 18 ARG A 20 ASN A 44 HIS A 139 SITE 2 AC3 12 CYS A 221 LEU A 222 ALA A 252 HIS A 254 SITE 3 AC3 12 ALA A 266 GLY A 267 ZN A 400 HOH A 420 CRYST1 72.610 72.610 176.120 90.00 90.00 90.00 P 41 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 0.013772 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013772 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005678 0.00000