HEADER COMPLEX (ISOMERASE/PEPTIDE) 24-NOV-95 2CSM TITLE TYR-BOUND T-STATE OF YEAST CHORISMATE MUTASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: CHORISMATE MUTASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: CHORISMATE PYRUVATE MUTASE; COMPND 5 EC: 5.4.99.5 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE; SOURCE 3 ORGANISM_COMMON: BAKER'S YEAST; SOURCE 4 ORGANISM_TAXID: 4932 KEYWDS ALLOSTERIC PROTEIN, COMPLEX (ISOMERASE-PEPTIDE), COMPLEX (ISOMERASE- KEYWDS 2 PEPTIDE) COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR N.STRAETER,K.HAKANSSON,W.N.LIPSCOMB REVDAT 3 14-FEB-24 2CSM 1 REMARK REVDAT 2 24-FEB-09 2CSM 1 VERSN REVDAT 1 23-DEC-96 2CSM 0 JRNL AUTH N.STRATER,K.HAKANSSON,G.SCHNAPPAUF,G.BRAUS,W.N.LIPSCOMB JRNL TITL CRYSTAL STRUCTURE OF THE T STATE OF ALLOSTERIC YEAST JRNL TITL 2 CHORISMATE MUTASE AND COMPARISON WITH THE R STATE. JRNL REF PROC.NATL.ACAD.SCI.USA V. 93 3330 1996 JRNL REFN ISSN 0027-8424 JRNL PMID 8622937 JRNL DOI 10.1073/PNAS.93.8.3330 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH Y.XUE,W.N.LIPSCOMB REMARK 1 TITL LOCATION OF THE ACTIVE SITE OF ALLOSTERIC CHORISMATE MUTASE REMARK 1 TITL 2 FROM SACCHAROMYCES CEREVISIAE, AND COMMENTS ON THE CATALYTIC REMARK 1 TITL 3 AND REGULATORY MECHANISMS REMARK 1 REF PROC.NATL.ACAD.SCI.USA V. 92 10595 1995 REMARK 1 REFN ISSN 0027-8424 REMARK 1 REFERENCE 2 REMARK 1 AUTH Y.XUE,W.N.LIPSCOMB,R.GRAF,G.SCHNAPPAUF,G.BRAUS REMARK 1 TITL THE CRYSTAL STRUCTURE OF ALLOSTERIC CHORISMATE MUTASE AT REMARK 1 TITL 2 2.2-A RESOLUTION REMARK 1 REF PROC.NATL.ACAD.SCI.USA V. 91 10814 1994 REMARK 1 REFN ISSN 0027-8424 REMARK 2 REMARK 2 RESOLUTION. 2.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.1 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 7.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 92.1 REMARK 3 NUMBER OF REFLECTIONS : 8964 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING SET) : 0.213 REMARK 3 FREE R VALUE : 0.321 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2012 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 13 REMARK 3 SOLVENT ATOMS : 31 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 22.40 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.35 REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.007 REMARK 3 BOND ANGLES (DEGREES) : 1.600 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 19.40 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.300 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL 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 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2CSM COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 100 THE DEPOSITION ID IS D_1000177952. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-OCT-95 REMARK 200 TEMPERATURE (KELVIN) : 123 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : NULL REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : NULL 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 : NULL REMARK 200 DETECTOR MANUFACTURER : SIEMENS REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 9401 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.800 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 (%) : 99.1 REMARK 200 DATA REDUNDANCY : 3.100 REMARK 200 R MERGE (I) : 0.06900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: X-PLOR 3.1 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 59.11 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.01 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 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+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 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 58.05000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 39.30000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 39.30000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 87.07500 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 39.30000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 39.30000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 29.02500 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 39.30000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 39.30000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 87.07500 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 39.30000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 39.30000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 29.02500 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 58.05000 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 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 157.20000 REMARK 350 BIOMT2 2 -1.000000 0.000000 0.000000 157.20000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 58.05000 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 ASP A 215 REMARK 465 PRO A 216 REMARK 465 THR A 217 REMARK 465 ASN A 218 REMARK 465 GLU A 219 REMARK 465 SER A 220 REMARK 465 GLY A 221 REMARK 465 GLU A 222 REMARK 465 ARG A 223 REMARK 465 GLU A 255 REMARK 465 GLU A 256 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 SER A 34 5.07 -68.57 REMARK 500 HIS A 47 67.71 37.97 REMARK 500 PRO A 53 103.12 -45.79 REMARK 500 ASN A 54 3.43 55.38 REMARK 500 SER A 58 173.32 -56.22 REMARK 500 ARG A 73 -9.67 -59.69 REMARK 500 PRO A 80 -4.70 -59.96 REMARK 500 LYS A 89 -1.79 -141.78 REMARK 500 ILE A 103 -51.70 -122.32 REMARK 500 ASP A 172 66.67 -157.02 REMARK 500 TYR A 212 -78.12 -62.28 REMARK 500 ARG A 252 36.43 -93.14 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: REG REMARK 800 EVIDENCE_CODE: UNKNOWN REMARK 800 SITE_DESCRIPTION: REGULATORY, ALLOSTERIC SITE. ONLY POLAR CONTACTS REMARK 800 TO TYR ARE LISTED. RESIDUES 138 - 145 MUST BE TRANSFORMED TO REMARK 800 GENERATE THE SECOND SUBUNIT OF THE DIMER IN ORDER TO BUILD A REMARK 800 COMPLETE REGULATORY SITE. REMARK 800 REMARK 800 SITE_IDENTIFIER: CAT REMARK 800 EVIDENCE_CODE: UNKNOWN REMARK 800 SITE_DESCRIPTION: PRESUMED CATALYTIC SITE. REMARK 800 REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE TYR A 300 DBREF 2CSM A 1 256 UNP P32178 CHMU_YEAST 1 256 SEQRES 1 A 256 MET ASP PHE THR LYS PRO GLU THR VAL LEU ASN LEU GLN SEQRES 2 A 256 ASN ILE ARG ASP GLU LEU VAL ARG MET GLU ASP SER ILE SEQRES 3 A 256 ILE PHE LYS PHE ILE GLU ARG SER HIS PHE ALA THR CYS SEQRES 4 A 256 PRO SER VAL TYR GLU ALA ASN HIS PRO GLY LEU GLU ILE SEQRES 5 A 256 PRO ASN PHE LYS GLY SER PHE LEU ASP TRP ALA LEU SER SEQRES 6 A 256 ASN LEU GLU ILE ALA HIS SER ARG ILE ARG ARG PHE GLU SEQRES 7 A 256 SER PRO ASP GLU THR PRO PHE PHE PRO ASP LYS ILE GLN SEQRES 8 A 256 LYS SER PHE LEU PRO SER ILE ASN TYR PRO GLN ILE LEU SEQRES 9 A 256 ALA PRO TYR ALA PRO GLU VAL ASN TYR ASN ASP LYS ILE SEQRES 10 A 256 LYS LYS VAL TYR ILE GLU LYS ILE ILE PRO LEU ILE SER SEQRES 11 A 256 LYS ARG ASP GLY ASP ASP LYS ASN ASN PHE GLY SER VAL SEQRES 12 A 256 ALA THR ARG ASP ILE GLU CYS LEU GLN SER LEU SER ARG SEQRES 13 A 256 ARG ILE HIS PHE GLY LYS PHE VAL ALA GLU ALA LYS PHE SEQRES 14 A 256 GLN SER ASP ILE PRO LEU TYR THR LYS LEU ILE LYS SER SEQRES 15 A 256 LYS ASP VAL GLU GLY ILE MET LYS ASN ILE THR ASN SER SEQRES 16 A 256 ALA VAL GLU GLU LYS ILE LEU GLU ARG LEU THR LYS LYS SEQRES 17 A 256 ALA GLU VAL TYR GLY VAL ASP PRO THR ASN GLU SER GLY SEQRES 18 A 256 GLU ARG ARG ILE THR PRO GLU TYR LEU VAL LYS ILE TYR SEQRES 19 A 256 LYS GLU ILE VAL ILE PRO ILE THR LYS GLU VAL GLU VAL SEQRES 20 A 256 GLU TYR LEU LEU ARG ARG LEU GLU GLU HET TYR A 300 13 HETNAM TYR TYROSINE FORMUL 2 TYR C9 H11 N O3 FORMUL 3 HOH *31(H2 O) HELIX 1 1 PRO A 6 VAL A 9 1 4 HELIX 2 2 LEU A 12 HIS A 35 1 24 HELIX 3 3 PRO A 40 VAL A 42 5 3 HELIX 4 4 PHE A 59 ILE A 74 1 16 HELIX 5 5 ARG A 76 GLU A 78 5 3 HELIX 6 6 PRO A 87 LYS A 89 5 3 HELIX 7 7 PRO A 106 GLU A 110 5 5 HELIX 8 8 ASN A 114 GLU A 123 1 10 HELIX 9 9 ILE A 126 ILE A 129 1 4 HELIX 10 10 LYS A 137 SER A 182 5 46 HELIX 11 11 VAL A 185 ASN A 191 1 7 HELIX 12 12 SER A 195 TYR A 212 1 18 SITE 1 REG 7 ASN A 138 ASN A 139 GLY A 141 SER A 142 SITE 2 REG 7 THR A 145 ARG A 75 ARG A 76 SITE 1 CAT 7 ARG A 16 LYS A 168 ASN A 194 GLU A 198 SITE 2 CAT 7 GLU A 246 THR A 242 ARG A 157 SITE 1 AC1 7 ILE A 74 ARG A 75 ARG A 76 ASN A 139 SITE 2 AC1 7 GLY A 141 SER A 142 THR A 145 CRYST1 78.600 78.600 116.100 90.00 90.00 90.00 P 43 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 0.012723 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012723 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008613 0.00000