HEADER LYASE 22-JUN-04 1TT8 TITLE CHORISMATE LYASE WITH PRODUCT, 1.0 A RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: CHORISMATE-PYRUVATE 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,B4039; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PSE380 KEYWDS NEW FOLD, UBIQUINONE PATHWAY, 123654 ANTIPARALLEL SHEET, LYASE EXPDTA X-RAY DIFFRACTION AUTHOR D.T.GALLAGHER,M.MAYHEW,M.J.HOLDEN,V.VILKER,A.HOWARD REVDAT 5 23-AUG-23 1TT8 1 REMARK REVDAT 4 27-OCT-21 1TT8 1 REMARK SEQADV REVDAT 3 11-OCT-17 1TT8 1 REMARK REVDAT 2 09-DEC-08 1TT8 1 JRNL VERSN REVDAT 1 28-DEC-04 1TT8 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. 1.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : SHELXL-97 REMARK 3 AUTHORS : G.M.SHELDRICK REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 8.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 86.6 REMARK 3 CROSS-VALIDATION METHOD : FREE R REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (NO CUTOFF). REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : 0.123 REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.120 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.153 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : 3.400 REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 2175 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 63630 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : 0.118 REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : 0.116 REMARK 3 FREE R VALUE (F>4SIG(F)) : 0.149 REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : 3.400 REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : 1987 REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : 58227 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 : 371 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : 1689.0 REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : 1360.0 REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : 3 REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : 15076 REMARK 3 NUMBER OF RESTRAINTS : 17545 REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.017 REMARK 3 ANGLE DISTANCES (A) : 0.035 REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : 0.000 REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : 0.032 REMARK 3 ZERO CHIRAL VOLUMES (A**3) : 0.108 REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : 0.089 REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : 0.065 REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : 0.006 REMARK 3 SIMILAR ADP COMPONENTS (A**2) : 0.038 REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : 0.090 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED: NULL REMARK 3 REMARK 3 STEREOCHEMISTRY TARGET VALUES : ENGH AND HUBER REMARK 3 SPECIAL CASE: NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: ANISOTROPIC REFINEMENT REDUCED FREE R REMARK 3 (NO CUTOFF) BY 0.02 REMARK 4 REMARK 4 1TT8 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 14-JUL-04. REMARK 100 THE DEPOSITION ID IS D_1000022885. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-MAY-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) : 0.7469 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : DOUBLE MIRROR REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : X-GEN REMARK 200 DATA SCALING SOFTWARE : X-GEN REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 88226 REMARK 200 RESOLUTION RANGE HIGH (A) : 0.920 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 (%) : 0.9 REMARK 200 DATA REDUNDANCY : 4.600 REMARK 200 R MERGE (I) : 0.06600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 25.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 0.92 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 0.94 REMARK 200 COMPLETENESS FOR SHELL (%) : 0.9 REMARK 200 DATA REDUNDANCY IN SHELL : 1.70 REMARK 200 R MERGE FOR SHELL (I) : 0.26200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: SHELX REMARK 200 STARTING MODEL: 1FW9 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 30.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.80 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 26% PEG4K, 80 MM HEPES, 5%(V/V) REMARK 280 ISOPROPANOL, PH 7.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 297K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,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 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 ENZYME IS MONOMERIC. THIS ENTRY IS FOR ONE 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: 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 OE1 GLU A 52 O HOH A 478 2.13 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 ASP A 21 CB - CG - OD1 ANGL. DEV. = 7.2 DEGREES REMARK 500 MET A 49 CG - SD - CE ANGL. DEV. = 12.4 DEGREES REMARK 500 ARG A 51 NH1 - CZ - NH2 ANGL. DEV. = 6.9 DEGREES REMARK 500 ARG A 51 NE - CZ - NH2 ANGL. DEV. = -6.1 DEGREES REMARK 500 ARG A 76 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 ARG A 133 NE - CZ - NH2 ANGL. DEV. = -4.3 DEGREES REMARK 500 ARG A 141 NE - CZ - NH2 ANGL. DEV. = -3.3 DEGREES REMARK 500 ARG A 145 NE - CZ - NH2 ANGL. DEV. = -3.7 DEGREES 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 400 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1FW9 RELATED DB: PDB REMARK 900 CHORISMATE LYASE WITH BOUND PRODUCT DBREF 1TT8 A 1 164 UNP P26602 UBIC_ECOLI 1 164 SEQADV 1TT8 SER A 14 UNP P26602 CYS 14 ENGINEERED MUTATION SEQADV 1TT8 SER A 81 UNP P26602 CYS 81 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 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 400 10 HETNAM PHB P-HYDROXYBENZOIC ACID FORMUL 2 PHB C7 H6 O3 FORMUL 3 HOH *371(H2 O) HELIX 1 1 HIS A 2 LEU A 11 1 10 HELIX 2 2 ASP A 21 LEU A 30 1 10 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 LYS A 108 5 9 HELIX 8 8 GLY A 115 PHE A 119 5 5 SHEET 1 A 6 VAL A 45 VAL A 55 0 SHEET 2 A 6 TYR A 73 ALA A 82 -1 O GLU A 77 N ARG A 51 SHEET 3 A 6 GLU A 85 PRO A 95 -1 O LEU A 88 N LEU A 80 SHEET 4 A 6 LYS A 149 PHE A 157 -1 O LEU A 152 N VAL A 93 SHEET 5 A 6 LEU A 137 LEU A 146 -1 N ARG A 140 O GLU A 155 SHEET 6 A 6 LEU A 124 ASP A 134 -1 N GLU A 130 O ARG A 141 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 401 CRYST1 31.315 33.849 39.776 67.57 87.83 65.66 P 1 1 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 0.031934 -0.014445 0.005019 0.00000 SCALE2 0.000000 0.032425 -0.014233 0.00000 SCALE3 0.000000 0.000000 0.027476 0.00000