PDB Short entry for 1JUL HEADER LYASE 03-MAY-96 1JUL TITLE INDOLE-3-GLYCEROLPHOSPHATE SYNTHASE FROM SULFOLOBUS SOLFATARICUS IN A TITLE 2 SECOND ORTHORHOMBIC CRYSTAL FORM COMPND MOL_ID: 1; COMPND 2 MOLECULE: INDOLE-3-GLYCEROL PHOSPHATE SYNTHASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: IGPS; COMPND 5 EC: 4.1.1.48; COMPND 6 ENGINEERED: YES; COMPND 7 OTHER_DETAILS: SECOND ORTHORHOMBIC CRYSTAL FORM SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SULFOLOBUS SOLFATARICUS; SOURCE 3 ORGANISM_TAXID: 2287; SOURCE 4 STRAIN: M4; SOURCE 5 GENE: TRPC; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PDS SS-1; SOURCE 9 EXPRESSION_SYSTEM_GENE: TRPC KEYWDS THERMOPHILE, TIM-BARREL, TRYPTOPHAN BIOSYNTHESIS, LYASE EXPDTA X-RAY DIFFRACTION AUTHOR T.R.KNOECHEL,M.HENNIG,A.MERZ,B.DARIMONT,K.KIRSCHNER,J.N.JANSONIUS REVDAT 3 09-AUG-23 1JUL 1 REMARK REVDAT 2 24-FEB-09 1JUL 1 VERSN REVDAT 1 07-JUL-97 1JUL 0 JRNL AUTH T.R.KNOCHEL,M.HENNIG,A.MERZ,B.DARIMONT,K.KIRSCHNER, JRNL AUTH 2 J.N.JANSONIUS JRNL TITL THE CRYSTAL STRUCTURE OF INDOLE-3-GLYCEROL PHOSPHATE JRNL TITL 2 SYNTHASE FROM THE HYPERTHERMOPHILIC ARCHAEON SULFOLOBUS JRNL TITL 3 SOLFATARICUS IN THREE DIFFERENT CRYSTAL FORMS: EFFECTS OF JRNL TITL 4 IONIC STRENGTH. JRNL REF J.MOL.BIOL. V. 262 502 1996 JRNL REFN ISSN 0022-2836 JRNL PMID 8893859 JRNL DOI 10.1006/JMBI.1996.0531 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH M.HENNIG,B.DARIMONT,R.STERNER,K.KIRSCHNER,J.N.JANSONIUS REMARK 1 TITL 2.0 A STRUCTURE OF INDOLE-3-GLYCEROL PHOSPHATE SYNTHASE FROM REMARK 1 TITL 2 THE HYPERTHERMOPHILE SULFOLOBUS SOLFATARICUS: POSSIBLE REMARK 1 TITL 3 DETERMINANTS OF PROTEIN STABILITY REMARK 1 REF STRUCTURE V. 3 1295 1995 REMARK 1 REFN ISSN 0969-2126 REMARK 2 REMARK 2 RESOLUTION. 2.00 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) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 12.00 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) (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 23719 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) : 0.176 REMARK 3 FREE R VALUE : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL 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 : 2003 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 12 REMARK 3 SOLVENT ATOMS : 251 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 19.90 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) : NULL 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) : 0.009 REMARK 3 BOND ANGLES (DEGREES) : 1.920 REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL 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 1JUL 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_1000174375. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-JAN-95 REMARK 200 TEMPERATURE (KELVIN) : 277 REMARK 200 PH : 6.5 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 : GRAPHITE(002) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : CCP4 (ROTAVATA) REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 27656 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 13.400 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 200 DATA REDUNDANCY : 3.300 REMARK 200 R MERGE (I) : 0.07800 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 7.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.06 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 3.20 REMARK 200 R MERGE FOR SHELL (I) : 0.25600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.900 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: X-PLOR 3.1 REMARK 200 STARTING MODEL: PDB ENTRY 1IGS REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 60.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.00 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PH 6.5 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 31.30000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 37.10000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 37.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 37.10000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 31.30000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 37.00000 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 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 MET A 1 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 ARG A 23 CD NE CZ NH1 NH2 REMARK 480 LYS A 42 CD CE NZ REMARK 480 GLU A 63 CG CD OE1 OE2 REMARK 480 LYS A 224 CG CD CE 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 TYR A 76 -35.85 -130.93 REMARK 500 SER A 211 144.91 71.71 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 MES A 1000 DBREF 1JUL A 1 248 UNP Q06121 TRPC_SULSO 1 248 SEQRES 1 A 248 MET PRO ARG TYR LEU LYS GLY TRP LEU LYS ASP VAL VAL SEQRES 2 A 248 GLN LEU SER LEU ARG ARG PRO SER PHE ARG ALA SER ARG SEQRES 3 A 248 GLN ARG PRO ILE ILE SER LEU ASN GLU ARG ILE LEU GLU SEQRES 4 A 248 PHE ASN LYS ARG ASN ILE THR ALA ILE ILE ALA GLU TYR SEQRES 5 A 248 LYS ARG LYS SER PRO SER GLY LEU ASP VAL GLU ARG ASP SEQRES 6 A 248 PRO ILE GLU TYR SER LYS PHE MET GLU ARG TYR ALA VAL SEQRES 7 A 248 GLY LEU SER ILE LEU THR GLU GLU LYS TYR PHE ASN GLY SEQRES 8 A 248 SER TYR GLU THR LEU ARG LYS ILE ALA SER SER VAL SER SEQRES 9 A 248 ILE PRO ILE LEU MET LYS ASP PHE ILE VAL LYS GLU SER SEQRES 10 A 248 GLN ILE ASP ASP ALA TYR ASN LEU GLY ALA ASP THR VAL SEQRES 11 A 248 LEU LEU ILE VAL LYS ILE LEU THR GLU ARG GLU LEU GLU SEQRES 12 A 248 SER LEU LEU GLU TYR ALA ARG SER TYR GLY MET GLU PRO SEQRES 13 A 248 LEU ILE GLU ILE ASN ASP GLU ASN ASP LEU ASP ILE ALA SEQRES 14 A 248 LEU ARG ILE GLY ALA ARG PHE ILE GLY ILE ASN SER ARG SEQRES 15 A 248 ASP LEU GLU THR LEU GLU ILE ASN LYS GLU ASN GLN ARG SEQRES 16 A 248 LYS LEU ILE SER MET ILE PRO SER ASN VAL VAL LYS VAL SEQRES 17 A 248 ALA GLU SER GLY ILE SER GLU ARG ASN GLU ILE GLU GLU SEQRES 18 A 248 LEU ARG LYS LEU GLY VAL ASN ALA PHE LEU ILE GLY SER SEQRES 19 A 248 SER LEU MET ARG ASN PRO GLU LYS ILE LYS GLU PHE ILE SEQRES 20 A 248 LEU HET MES A1000 12 HETNAM MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID FORMUL 2 MES C6 H13 N O4 S FORMUL 3 HOH *251(H2 O) HELIX 1 1 GLY A 7 LEU A 17 1 11 HELIX 2 2 LEU A 33 ARG A 43 1 11 HELIX 3 3 PRO A 66 ARG A 75 1 10 HELIX 4 4 TYR A 93 ALA A 100 1 8 HELIX 5 5 GLU A 116 LEU A 125 1 10 HELIX 6 6 VAL A 134 ILE A 136 5 3 HELIX 7 7 GLU A 139 TYR A 152 1 14 HELIX 8 8 GLU A 163 ARG A 171 1 9 HELIX 9 9 LYS A 191 MET A 200 1 10 HELIX 10 10 ARG A 216 LEU A 225 1 10 HELIX 11 11 SER A 234 ARG A 238 1 5 HELIX 12 12 PRO A 240 PHE A 246 5 7 SHEET 1 A 8 PRO A 106 LYS A 110 0 SHEET 2 A 8 GLY A 79 LEU A 83 1 N LEU A 80 O PRO A 106 SHEET 3 A 8 ILE A 48 TYR A 52 1 N ALA A 50 O GLY A 79 SHEET 4 A 8 ALA A 229 ILE A 232 1 N PHE A 230 O ILE A 49 SHEET 5 A 8 VAL A 206 GLU A 210 1 N ALA A 209 O ALA A 229 SHEET 6 A 8 PHE A 176 ASN A 180 1 N ILE A 177 O VAL A 206 SHEET 7 A 8 LEU A 157 ILE A 160 1 N ILE A 158 O GLY A 178 SHEET 8 A 8 LEU A 131 ILE A 133 1 N LEU A 132 O LEU A 157 SITE 1 AC1 14 GLU A 51 LYS A 53 LYS A 110 GLU A 210 SITE 2 AC1 14 SER A 211 GLY A 212 GLY A 233 SER A 234 SITE 3 AC1 14 HOH A 348 HOH A 364 HOH A 406 HOH A 412 SITE 4 AC1 14 HOH A 532 HOH A 533 CRYST1 62.600 74.000 74.200 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 0.015974 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013514 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013477 0.00000