HEADER LYASE 15-NOV-00 1G81 TITLE CHORISMATE LYASE WITH BOUND PRODUCT, ORTHORHOMBIC CRYSTAL FORM COMPND MOL_ID: 1; COMPND 2 MOLECULE: CHORISMATE LYASE; COMPND 3 CHAIN: A; COMPND 4 EC: 4.-.-.-; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES 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 NEW FOLD, UBIQUINONE PATHWAY, 123654 ANTIPARALLEL SHEET TOPOLOGY, KEYWDS 2 PRODUCT INHIBITION, LYASE EXPDTA X-RAY DIFFRACTION AUTHOR D.T.GALLAGHER,M.MAYHEW,M.J.HOLDEN,V.L.VILKER,A.HOWARD REVDAT 7 07-FEB-24 1G81 1 REMARK REVDAT 6 27-OCT-21 1G81 1 REMARK SEQADV REVDAT 5 04-OCT-17 1G81 1 REMARK REVDAT 4 24-FEB-09 1G81 1 VERSN REVDAT 3 01-APR-03 1G81 1 JRNL REVDAT 2 22-AUG-01 1G81 1 JRNL REVDAT 1 15-MAY-01 1G81 0 JRNL AUTH D.T.GALLAGHER,M.MAYHEW,M.J.HOLDEN,A.HOWARD,K.J.KIM, JRNL AUTH 2 V.L.VILKER JRNL TITL THE CRYSTAL STRUCTURE OF CHORISMATE LYASE SHOWS A NEW FOLD JRNL TITL 2 AND A TIGHTLY RETAINED PRODUCT. JRNL REF PROTEINS V. 44 304 2001 JRNL REFN ISSN 0887-3585 JRNL PMID 11455603 JRNL DOI 10.1002/PROT.1095 REMARK 2 REMARK 2 RESOLUTION. 1.71 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) : 1.71 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 8.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 481823.140 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 94.8 REMARK 3 NUMBER OF REFLECTIONS : 15223 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : EVERY NTH REMARK 3 R VALUE (WORKING SET) : 0.202 REMARK 3 FREE R VALUE : 0.253 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 772 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.009 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) : 1.70 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.78 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 73.00 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 1398 REMARK 3 BIN R VALUE (WORKING SET) : 0.2420 REMARK 3 BIN FREE R VALUE : 0.2610 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 4.80 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 71 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.031 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1315 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 10 REMARK 3 SOLVENT ATOMS : 140 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 14.10 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 16.20 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.87000 REMARK 3 B22 (A**2) : 3.49000 REMARK 3 B33 (A**2) : -4.36000 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) : 0.18 REMARK 3 ESD FROM SIGMAA (A) : -0.1 REMARK 3 LOW RESOLUTION CUTOFF (A) : 8.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.24 REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.017 REMARK 3 BOND ANGLES (DEGREES) : 1.900 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 26.30 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.200 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) : 1.310 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 1.850 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.180 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 3.220 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.44 REMARK 3 BSOL : 74.79 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.PARAM REMARK 3 PARAMETER FILE 3 : PHB.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 : PHB.TOP REMARK 3 TOPOLOGY FILE 4 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1G81 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 21-NOV-00. REMARK 100 THE DEPOSITION ID IS D_1000012349. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 28-FEB-00 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 17-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9879 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : X-GEN REMARK 200 DATA SCALING SOFTWARE : X-GEN REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 15812 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 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 (%) : 95.0 REMARK 200 DATA REDUNDANCY : 4.000 REMARK 200 R MERGE (I) : 0.04000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 16.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.76 REMARK 200 COMPLETENESS FOR SHELL (%) : 83.0 REMARK 200 DATA REDUNDANCY IN SHELL : 3.10 REMARK 200 R MERGE FOR SHELL (I) : 0.12000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SIRAS REMARK 200 SOFTWARE USED: PHASES REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 36.55 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.94 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 26% PEG 4K, 80 MM HEPES, 5% REMARK 280 ISOPROPANOL, 5MM PHB, PH 7.0, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 297K 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 15.98100 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 35.94700 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 31.49150 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 35.94700 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 15.98100 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 31.49150 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: ENZYME IS A MONOMER 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 2 143.29 -176.83 REMARK 500 GLU A 31 55.64 -90.59 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 PHB A 199 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1FW9 RELATED DB: PDB REMARK 900 1FW9 IS A DOUBLE MUTANT, TRICLINIC CRYSTAL FORM, HIGHER RESOLUTION REMARK 900 (1.4 A) REMARK 900 RELATED ID: 1G1B RELATED DB: PDB REMARK 900 1G1B IS THE WILD-TYPE, IN A MONOCLINIC CRYSTAL FORM AT 2.0 A RESOL. DBREF 1G81 A 1 164 UNP P26602 UBIC_ECOLI 1 164 SEQADV 1G81 SER A 14 UNP P26602 CYS 14 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 CYS ALA ASP GLY GLU PRO TRP LEU ALA GLY 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 PHB A 199 10 HETNAM PHB P-HYDROXYBENZOIC ACID FORMUL 2 PHB C7 H6 O3 FORMUL 3 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 PHE A 119 5 5 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 N LEU A 137 O ASP A 134 SHEET 4 A 7 LYS A 149 PHE A 157 -1 O LYS A 149 N LEU A 146 SHEET 5 A 7 GLU A 85 PRO A 95 -1 O ALA A 89 N LEU A 156 SHEET 6 A 7 TYR A 73 ALA A 82 -1 N TRP A 74 O VAL A 94 SHEET 7 A 7 VAL A 45 VAL A 55 -1 O SER A 46 N CYS A 81 SITE 1 AC1 11 SER A 33 MET A 34 THR A 35 ARG A 76 SITE 2 AC1 11 ILE A 78 LEU A 80 LEU A 88 PRO A 113 SITE 3 AC1 11 LEU A 114 GLU A 155 HOH A 203 CRYST1 31.962 62.983 71.894 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 0.031287 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015877 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013909 0.00000