10 20 30 40 50 60 70 80 1TT8 - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER 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, KEYWDS 2 LYASE
EXPDTA X-RAY DIFFRACTION
AUTHOR D.T.GALLAGHER,M.MAYHEW,M.J.HOLDEN,V.VILKER,A.HOWARD
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, JRNL AUTH 2 M.MAYHEW,S.KAISTHA,D.T.GALLAGHER JRNL TITL STRUCTURAL ANALYSIS OF LIGAND BINDING AND JRNL TITL 2 CATALYSIS IN 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 1
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 : 2700 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 : 1689.00 REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : 1360.00 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 REMARK 3 R (NO CUTOFF) BY 0.02
REMARK 4 REMARK 4 1TT8 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 14-JUL-04. REMARK 100 THE RCSB ID CODE IS RCSB022885.
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 <I/SIGMA(I)> 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 <I/SIGMA(I)> 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, REMARK 280 TEMPERATURE 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. = 7.1 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 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 692 DISTANCE = 7.16 ANGSTROMS REMARK 525 HOH A 694 DISTANCE = 6.95 ANGSTROMS REMARK 525 HOH A 701 DISTANCE = 7.15 ANGSTROMS
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 SEQADV 1TT8 SER A 81 UNP P26602 CYS 81 ENGINEERED
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