HEADER LYASE 30-SEP-04 1XLR TITLE CHORISMATE LYASE WITH INHIBITOR VANILLATE COMPND MOL_ID: 1; COMPND 2 MOLECULE: CHORISMATE--PYRUVATE LYASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: CHORISMATE LYASE; COMPND 5 EC: 4.1.3.40; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES; COMPND 8 OTHER_DETAILS: MUTATIONS: C14S, C81S, G90A SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562; SOURCE 4 GENE: UBIC; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS SECONDARY INHIBITOR SITE, LYASE EXPDTA X-RAY DIFFRACTION AUTHOR D.T.GALLAGHER,N.SMITH REVDAT 5 11-OCT-17 1XLR 1 REMARK REVDAT 4 13-JUL-11 1XLR 1 VERSN REVDAT 3 26-JAN-11 1XLR 1 HETSYN REVDAT 2 09-DEC-08 1XLR 1 JRNL VERSN REVDAT 1 09-NOV-04 1XLR 0 JRNL AUTH N.SMITH,A.E.ROITBERG,E.RIVERA,A.HOWARD,M.J.HOLDEN,M.MAYHEW, JRNL AUTH 2 S.KAISTHA,D.T.GALLAGHER JRNL TITL STRUCTURAL ANALYSIS OF LIGAND BINDING AND CATALYSIS IN JRNL TITL 2 CHORISMATE LYASE. JRNL REF ARCH.BIOCHEM.BIOPHYS. V. 445 72 2006 JRNL REFN ISSN 0003-9861 JRNL PMID 16343413 JRNL DOI 10.1016/J.ABB.2005.10.026 REMARK 2 REMARK 2 RESOLUTION. 1.94 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.0 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.94 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 7.98 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 122521.120 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 91.6 REMARK 3 NUMBER OF REFLECTIONS : 10792 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING SET) : 0.173 REMARK 3 FREE R VALUE : 0.236 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.200 REMARK 3 FREE R VALUE TEST SET COUNT : 557 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.010 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 8 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.94 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.02 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 70.20 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 986 REMARK 3 BIN R VALUE (WORKING SET) : 0.2530 REMARK 3 BIN FREE R VALUE : 0.2850 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.20 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 54 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.039 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1316 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 24 REMARK 3 SOLVENT ATOMS : 140 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 15.30 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 22.00 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.31000 REMARK 3 B22 (A**2) : 4.08000 REMARK 3 B33 (A**2) : -2.77000 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 COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.19 REMARK 3 ESD FROM SIGMAA (A) : 0.21 REMARK 3 LOW RESOLUTION CUTOFF (A) : 12.0 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.26 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.19 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.022 REMARK 3 BOND ANGLES (DEGREES) : 2.200 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 26.30 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.390 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.610 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.450 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.430 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 3.690 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.40 REMARK 3 BSOL : 59.28 REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 3 : VAN.PARAM REMARK 3 PARAMETER FILE 4 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : WATER.TOP REMARK 3 TOPOLOGY FILE 3 : VAN.TOP REMARK 3 TOPOLOGY FILE 4 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1XLR COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 02-NOV-04. REMARK 100 THE DEPOSITION ID IS D_1000030489. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-MAY-01 REMARK 200 TEMPERATURE (KELVIN) : 295 REMARK 200 PH : 7.0 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 : SIEMENS REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : AREA DETECTOR REMARK 200 DETECTOR MANUFACTURER : SIEMENS HI-STAR REMARK 200 INTENSITY-INTEGRATION SOFTWARE : X-GEN REMARK 200 DATA SCALING SOFTWARE : X-GEN REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 10973 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.930 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 92.0 REMARK 200 DATA REDUNDANCY : 5.100 REMARK 200 R MERGE (I) : 0.06100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.93 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.05 REMARK 200 COMPLETENESS FOR SHELL (%) : 74.0 REMARK 200 DATA REDUNDANCY IN SHELL : 1.90 REMARK 200 R MERGE FOR SHELL (I) : 0.20000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.900 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: CNS REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 34.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.90 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 25% PEG 4000, 80 MM HEPES, 5%(V/V) REMARK 280 ISOPROPANOL, 20MM VANILLATE, PH 7.0, VAPOR DIFFUSION, HANGING REMARK 280 DROP, TEMPERATURE 295K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-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 16.13500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 36.33500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 32.59500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 36.33500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 16.13500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 32.59500 REMARK 290 SMTRY3 4 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 300 REMARK: BIOLOGICAL UNIT IS A MONOMER, REMARK 300 EQUAL TO ONE ASYMMETRIC UNIT. 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: MONOMERIC 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 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 2 142.13 -175.09 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 73 0.08 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE VNL A 181 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE VNL A 182 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1FW9 RELATED DB: PDB REMARK 900 1.0 ANGSTROM STRUCTURE OF CHORISMATE LYASE WITH PRODUCT REMARK 900 RELATED ID: 1G1B RELATED DB: PDB REMARK 900 WILD-TYPE CHORISMATE LYASE WITH PRODUCT REMARK 900 RELATED ID: 1G81 RELATED DB: PDB REMARK 900 CHORISMATE LYASE WITH BOUND PRODUCT, ORTHORHOMBIC CRYSTAL FORM REMARK 900 RELATED ID: 1JD3 RELATED DB: PDB REMARK 900 CHORISMATE LYASE G90A MUTANT WITH PRODUCT DBREF 1XLR A 1 164 UNP P26602 UBIC_ECOLI 1 164 SEQADV 1XLR SER A 14 UNP P26602 CYS 14 ENGINEERED MUTATION SEQADV 1XLR SER A 81 UNP P26602 CYS 81 ENGINEERED MUTATION SEQADV 1XLR ALA A 90 UNP P26602 GLY 90 ENGINEERED MUTATION SEQRES 1 A 164 SER HIS PRO ALA LEU THR GLN LEU ARG ALA LEU ARG TYR SEQRES 2 A 164 SER LYS GLU ILE PRO ALA LEU ASP PRO GLN LEU LEU ASP SEQRES 3 A 164 TRP LEU LEU LEU GLU ASP SER MET THR LYS ARG PHE GLU SEQRES 4 A 164 GLN GLN GLY LYS THR VAL SER VAL THR MET ILE ARG GLU SEQRES 5 A 164 GLY PHE VAL GLU GLN ASN GLU ILE PRO GLU GLU LEU PRO SEQRES 6 A 164 LEU LEU PRO LYS GLU SER ARG TYR TRP LEU ARG GLU ILE SEQRES 7 A 164 LEU LEU SER ALA ASP GLY GLU PRO TRP LEU ALA ALA ARG SEQRES 8 A 164 THR VAL VAL PRO VAL SER THR LEU SER GLY PRO GLU LEU SEQRES 9 A 164 ALA LEU GLN LYS LEU GLY LYS THR PRO LEU GLY ARG TYR SEQRES 10 A 164 LEU PHE THR SER SER THR LEU THR ARG ASP PHE ILE GLU SEQRES 11 A 164 ILE GLY ARG ASP ALA GLY LEU TRP GLY ARG ARG SER ARG SEQRES 12 A 164 LEU ARG LEU SER GLY LYS PRO LEU LEU LEU THR GLU LEU SEQRES 13 A 164 PHE LEU PRO ALA SER PRO LEU TYR HET VNL A 181 24 HET VNL A 182 12 HETNAM VNL 4-HYDROXY-3-METHOXYBENZOATE HETSYN VNL VANILLATE FORMUL 2 VNL 2(C8 H7 O4 1-) FORMUL 4 HOH *140(H2 O) HELIX 1 1 HIS A 2 ALA A 10 1 9 HELIX 2 2 ASP A 21 LEU A 29 1 9 HELIX 3 3 MET A 34 GLN A 40 1 7 HELIX 4 4 GLU A 56 ILE A 60 5 5 HELIX 5 5 GLU A 63 LEU A 67 5 5 HELIX 6 6 SER A 97 LEU A 99 5 3 HELIX 7 7 SER A 100 LEU A 109 5 10 HELIX 8 8 GLY A 115 THR A 120 5 6 SHEET 1 A 7 ARG A 12 TYR A 13 0 SHEET 2 A 7 LEU A 124 ASP A 134 -1 O ARG A 133 N ARG A 12 SHEET 3 A 7 LEU A 137 LEU A 146 -1 O GLY A 139 N GLY A 132 SHEET 4 A 7 LYS A 149 PHE A 157 -1 O LEU A 153 N SER A 142 SHEET 5 A 7 GLU A 85 PRO A 95 -1 N ARG A 91 O THR A 154 SHEET 6 A 7 TYR A 73 ALA A 82 -1 N LEU A 80 O LEU A 88 SHEET 7 A 7 VAL A 45 VAL A 55 -1 N THR A 48 O LEU A 79 SITE 1 AC1 12 SER A 33 MET A 34 THR A 35 ARG A 76 SITE 2 AC1 12 ILE A 78 LEU A 80 ALA A 90 PRO A 113 SITE 3 AC1 12 LEU A 114 LEU A 153 GLU A 155 HOH A 201 SITE 1 AC2 9 GLU A 31 ASP A 32 SER A 33 ARG A 116 SITE 2 AC2 9 LEU A 124 ARG A 126 ARG A 140 LEU A 144 SITE 3 AC2 9 LEU A 153 CRYST1 32.270 65.190 72.670 90.00 90.00 90.00 P 21 21 21 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 0.030989 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015340 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013761 0.00000 MASTER 270 0 2 8 7 0 6 6 0 0 0 13 END