PDB Short entry for 1UJP HEADER LYASE 08-AUG-03 1UJP TITLE CRYSTAL STRUCTURE OF TRYPTOPHAN SYNTHASE A-SUBUNIT FROM THERMUS TITLE 2 THERMOPHILUS HB8 COMPND MOL_ID: 1; COMPND 2 MOLECULE: TRYPTOPHAN SYNTHASE ALPHA CHAIN; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: TRYPTOPHAN SYNTHASE A-SUBUNIT; COMPND 5 EC: 4.2.1.20; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: THERMUS THERMOPHILUS; SOURCE 3 ORGANISM_TAXID: 300852; SOURCE 4 STRAIN: HB8; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET11A KEYWDS TRYPTOPHAN SYNTHASE, TRYPTOPHAN, RIKEN STRUCTURAL GENOMICS/PROTEOMICS KEYWDS 2 INITIATIVE, RSGI, STRUCTURAL GENOMICS, LYASE EXPDTA X-RAY DIFFRACTION AUTHOR Y.ASADA,S.YOKOYAMA,S.KURAMITSU,M.MIYANO,N.KUNISHIMA,RIKEN STRUCTURAL AUTHOR 2 GENOMICS/PROTEOMICS INITIATIVE (RSGI) REVDAT 4 25-OCT-23 1UJP 1 REMARK REVDAT 3 13-JUL-11 1UJP 1 VERSN REVDAT 2 24-FEB-09 1UJP 1 VERSN REVDAT 1 26-AUG-03 1UJP 0 JRNL AUTH Y.ASADA,M.SAWANO,K.OGASAHARA,J.NAKAMURA,M.OTA,C.KUROISHI, JRNL AUTH 2 M.SUGAHARA,K.YUTANI,N.KUNISHIMA JRNL TITL STABILIZATION MECHANISM OF THE TRYPTOPHAN SYNTHASE JRNL TITL 2 ALPHA-SUBUNIT FROM THERMUS THERMOPHILUS HB8: X-RAY JRNL TITL 3 CRYSTALLOGRAPHIC ANALYSIS AND CALORIMETRY. JRNL REF J.BIOCHEM.(TOKYO) V. 138 343 2005 JRNL REFN ISSN 0021-924X JRNL PMID 16272128 JRNL DOI 10.1093/JB/MVI133 REMARK 2 REMARK 2 RESOLUTION. 1.34 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1 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) : 1.34 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 27.30 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 99.3 REMARK 3 NUMBER OF REFLECTIONS : 55414 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.203 REMARK 3 FREE R VALUE : 0.221 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 2621 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) : 1.34 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.40 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.40 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.2550 REMARK 3 BIN FREE R VALUE : 0.2710 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : 332 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.015 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1833 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 13 REMARK 3 SOLVENT ATOMS : 303 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 13.60 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 17.30 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.97000 REMARK 3 B22 (A**2) : 2.32000 REMARK 3 B33 (A**2) : -0.35000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 1.40000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.16 REMARK 3 ESD FROM SIGMAA (A) : 0.12 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.18 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.14 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.007 REMARK 3 BOND ANGLES (DEGREES) : 1.500 REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : ANISOTROPIC 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 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : 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 1UJP COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 12-AUG-03. REMARK 100 THE DEPOSITION ID IS D_1000005901. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-JUN-03 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL26B1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.8 REMARK 200 MONOCHROMATOR : BENDING MAGNET REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS V REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 55454 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.340 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : 3.600 REMARK 200 R MERGE (I) : 0.04500 REMARK 200 R SYM (I) : 0.04200 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 14.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.34 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.39 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 3.70 REMARK 200 R MERGE FOR SHELL (I) : 0.35600 REMARK 200 R SYM FOR SHELL (I) : 0.30400 REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.600 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: PDB ENTRY 1GEQ REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 40.18 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.07 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: AMMONIUM ACETATE, TRI-SODIUM CITRATE REMARK 280 DIHYDRATE, PEG 4000, GLYCEROL ANHYDROUS, PH 5.6, MICROBATCH, REMARK 280 TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 38.43400 REMARK 290 SMTRY3 2 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 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 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 PRO A 55 REMARK 465 LEU A 56 REMARK 465 GLY A 57 REMARK 465 ASP A 58 REMARK 465 THR A 177 REMARK 465 GLY A 178 REMARK 465 VAL A 179 REMARK 465 THR A 180 REMARK 465 GLY A 181 REMARK 465 MET A 182 REMARK 465 ARG A 183 REMARK 465 GLU A 184 REMARK 465 ARG A 185 REMARK 465 LEU A 186 REMARK 465 PRO A 187 REMARK 465 GLU A 188 REMARK 465 GLU A 257 REMARK 465 ALA A 258 REMARK 465 ASN A 259 REMARK 465 PRO A 260 REMARK 465 GLY A 261 REMARK 465 LEU A 262 REMARK 465 LYS A 263 REMARK 465 GLU A 264 REMARK 465 SER A 265 REMARK 465 SER A 266 REMARK 465 LYS A 267 REMARK 465 LYS A 268 REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 GLU A 30 CD OE1 OE2 REMARK 480 SER A 53 CB OG REMARK 480 ARG A 200 NE CZ NH1 NH2 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 ASP A 133 69.98 -151.49 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 CIT A 1001 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: TTK003000017.1 RELATED DB: TARGETDB DBREF 1UJP A 1 270 UNP P16608 TRPA_THET2 1 270 SEQRES 1 A 271 MET THR THR LEU GLU ALA PHE ALA LYS ALA ARG SER GLU SEQRES 2 A 271 GLY ARG ALA ALA LEU ILE PRO TYR LEU THR ALA GLY PHE SEQRES 3 A 271 PRO SER ARG GLU GLY PHE LEU GLN ALA VAL GLU GLU VAL SEQRES 4 A 271 LEU PRO TYR ALA ASP LEU LEU GLU ILE GLY LEU PRO TYR SEQRES 5 A 271 SER ASP PRO LEU GLY ASP GLY PRO VAL ILE GLN ARG ALA SEQRES 6 A 271 SER GLU LEU ALA LEU ARG LYS GLY MET SER VAL GLN GLY SEQRES 7 A 271 ALA LEU GLU LEU VAL ARG GLU VAL ARG ALA LEU THR GLU SEQRES 8 A 271 LYS PRO LEU PHE LEU MET THR TYR LEU ASN PRO VAL LEU SEQRES 9 A 271 ALA TRP GLY PRO GLU ARG PHE PHE GLY LEU PHE LYS GLN SEQRES 10 A 271 ALA GLY ALA THR GLY VAL ILE LEU PRO ASP LEU PRO PRO SEQRES 11 A 271 ASP GLU ASP PRO GLY LEU VAL ARG LEU ALA GLN GLU ILE SEQRES 12 A 271 GLY LEU GLU THR VAL PHE LEU LEU ALA PRO THR SER THR SEQRES 13 A 271 ASP ALA ARG ILE ALA THR VAL VAL ARG HIS ALA THR GLY SEQRES 14 A 271 PHE VAL TYR ALA VAL SER VAL THR GLY VAL THR GLY MET SEQRES 15 A 271 ARG GLU ARG LEU PRO GLU GLU VAL LYS ASP LEU VAL ARG SEQRES 16 A 271 ARG ILE LYS ALA ARG THR ALA LEU PRO VAL ALA VAL GLY SEQRES 17 A 271 PHE GLY VAL SER GLY LYS ALA THR ALA ALA GLN ALA ALA SEQRES 18 A 271 VAL ALA ASP GLY VAL VAL VAL GLY SER ALA LEU VAL ARG SEQRES 19 A 271 ALA LEU GLU GLU GLY ARG SER LEU ALA PRO LEU LEU GLN SEQRES 20 A 271 GLU ILE ARG GLN GLY LEU GLN ARG LEU GLU ALA ASN PRO SEQRES 21 A 271 GLY LEU LYS GLU SER SER LYS LYS PRO LEU PRO HET CIT A1001 13 HETNAM CIT CITRIC ACID FORMUL 2 CIT C6 H8 O7 FORMUL 3 HOH *303(H2 O) HELIX 1 1 THR A 2 GLU A 13 1 12 HELIX 2 2 SER A 28 LEU A 40 1 13 HELIX 3 3 PRO A 41 ALA A 43 5 3 HELIX 4 4 GLY A 59 LYS A 72 1 14 HELIX 5 5 SER A 75 THR A 90 1 16 HELIX 6 6 TYR A 99 GLY A 107 1 9 HELIX 7 7 GLY A 107 GLY A 119 1 13 HELIX 8 8 PRO A 129 GLU A 132 5 4 HELIX 9 9 ASP A 133 GLY A 144 1 12 HELIX 10 10 THR A 156 ARG A 165 1 10 HELIX 11 11 VAL A 190 ALA A 199 1 10 HELIX 12 12 GLY A 213 ALA A 221 1 9 HELIX 13 13 GLY A 229 GLU A 238 1 10 HELIX 14 14 SER A 241 GLN A 254 1 14 SHEET 1 A 9 GLU A 146 VAL A 148 0 SHEET 2 A 9 GLY A 122 ILE A 124 1 N VAL A 123 O VAL A 148 SHEET 3 A 9 LEU A 94 MET A 97 1 N LEU A 96 O ILE A 124 SHEET 4 A 9 LEU A 46 GLY A 49 1 N ILE A 48 O PHE A 95 SHEET 5 A 9 ALA A 17 THR A 23 1 N LEU A 22 O GLU A 47 SHEET 6 A 9 GLY A 225 VAL A 228 1 O VAL A 226 N ILE A 19 SHEET 7 A 9 VAL A 205 GLY A 208 1 N VAL A 207 O VAL A 227 SHEET 8 A 9 VAL A 171 VAL A 174 1 N ALA A 173 O ALA A 206 SHEET 9 A 9 LEU A 150 LEU A 151 1 N LEU A 151 O VAL A 174 CISPEP 1 PHE A 26 PRO A 27 0 -0.77 SITE 1 AC1 11 TYR A 21 TYR A 172 GLY A 208 PHE A 209 SITE 2 AC1 11 GLY A 210 GLY A 229 SER A 230 HOH A1009 SITE 3 AC1 11 HOH A1013 HOH A1087 HOH A1101 CRYST1 42.400 76.868 42.774 90.00 115.08 90.00 P 1 21 1 2 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 0.023585 0.000000 0.011038 0.00000 SCALE2 0.000000 0.013009 0.000000 0.00000 SCALE3 0.000000 0.000000 0.025812 0.00000