PDB Short entry for 1A53 HEADER SYNTHASE 19-FEB-98 1A53 TITLE COMPLEX OF INDOLE-3-GLYCEROLPHOSPHATE SYNTHASE FROM SULFOLOBUS TITLE 2 SOLFATARICUS WITH INDOLE-3-GLYCEROLPHOSPHATE AT 2.0 A RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: INDOLE-3-GLYCEROLPHOSPHATE SYNTHASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: IGPS; COMPND 5 EC: 4.1.1.48; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SULFOLOBUS SOLFATARICUS; SOURCE 3 ORGANISM_TAXID: 2287; SOURCE 4 GENE: TRPC; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI STR. K12 SUBSTR. W3110; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 316407; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: W3110; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: REPRESSOR PLASMID PDM; SOURCE 10 EXPRESSION_SYSTEM_GENE: TRPC KEYWDS SYNTHASE, THERMOSTABLE, TIM-BARREL EXPDTA X-RAY DIFFRACTION AUTHOR M.HENNIG,B.DARIMONT,K.KIRSCHNER,J.N.JANSONIUS REVDAT 5 02-AUG-23 1A53 1 REMARK REVDAT 4 09-FEB-11 1A53 1 REMARK REVDAT 3 24-FEB-09 1A53 1 VERSN REVDAT 2 01-APR-03 1A53 1 JRNL REVDAT 1 23-MAR-99 1A53 0 JRNL AUTH M.HENNIG,B.D.DARIMONT,J.N.JANSONIUS,K.KIRSCHNER JRNL TITL THE CATALYTIC MECHANISM OF INDOLE-3-GLYCEROL PHOSPHATE JRNL TITL 2 SYNTHASE: CRYSTAL STRUCTURES OF COMPLEXES OF THE ENZYME FROM JRNL TITL 3 SULFOLOBUS SOLFATARICUS WITH SUBSTRATE ANALOGUE, SUBSTRATE, JRNL TITL 4 AND PRODUCT. JRNL REF J.MOL.BIOL. V. 319 757 2002 JRNL REFN ISSN 0022-2836 JRNL PMID 12054868 JRNL DOI 10.1016/S0022-2836(02)00378-9 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) : 15.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 91.1 REMARK 3 NUMBER OF REFLECTIONS : 27283 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) : 0.159 REMARK 3 FREE R VALUE : 0.212 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 : 10 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.07 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 48.00 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 1705 REMARK 3 BIN R VALUE (WORKING SET) : 0.3030 REMARK 3 BIN FREE R VALUE : 0.3527 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 10.00 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 88 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 : 19 REMARK 3 SOLVENT ATOMS : 242 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 32.20 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 29.60 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) : 0.012 REMARK 3 BOND ANGLES (DEGREES) : 1.700 REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED 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 : PARAM19X.PRO REMARK 3 PARAMETER FILE 2 : PARHCSDX.PRO REMARK 3 PARAMETER FILE 3 : IGP.PRX REMARK 3 PARAMETER FILE 4 : NULL REMARK 3 TOPOLOGY FILE 1 : TOPH19X.PRO REMARK 3 TOPOLOGY FILE 2 : TOPHCSDX.PRO REMARK 3 TOPOLOGY FILE 3 : IGP.TPX REMARK 3 TOPOLOGY FILE 4 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1A53 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_1000170402. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-AUG-94 REMARK 200 TEMPERATURE (KELVIN) : 277 REMARK 200 PH : 5.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : ELLIOTT GX-21 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 (SCALA) REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 27283 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 15.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 91.1 REMARK 200 DATA REDUNDANCY : 5.100 REMARK 200 R MERGE (I) : 0.06300 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 10.0000 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) : 2.05 REMARK 200 COMPLETENESS FOR SHELL (%) : 48.0 REMARK 200 DATA REDUNDANCY IN SHELL : 4.40 REMARK 200 R MERGE FOR SHELL (I) : 0.39000 REMARK 200 R SYM FOR SHELL (I) : 0.39000 REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.600 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: 1IGS REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 68.50 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.91 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PH 5.5 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 28.95000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 52.10000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 36.90000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 52.10000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 28.95000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 36.90000 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 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 LYS A 6 CD CE NZ REMARK 480 ARG A 23 NH1 NH2 REMARK 480 LYS A 42 CE NZ REMARK 480 GLU A 63 OE1 OE2 REMARK 480 GLU A 94 OE1 OE2 REMARK 480 LYS A 98 NZ REMARK 480 ARG A 140 CG CD NE CZ NH1 NH2 REMARK 480 ARG A 216 NH1 NH2 REMARK 480 GLU A 220 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 SER A 211 142.64 81.76 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 IGP A 300 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1IGS RELATED DB: PDB REMARK 900 RELATED ID: 1LBF RELATED DB: PDB REMARK 900 RELATED ID: 1LBL RELATED DB: PDB DBREF 1A53 A 2 248 UNP Q06121 TRPC_SULSO 2 248 SEQRES 1 A 247 PRO ARG TYR LEU LYS GLY TRP LEU LYS ASP VAL VAL GLN SEQRES 2 A 247 LEU SER LEU ARG ARG PRO SER PHE ARG ALA SER ARG GLN SEQRES 3 A 247 ARG PRO ILE ILE SER LEU ASN GLU ARG ILE LEU GLU PHE SEQRES 4 A 247 ASN LYS ARG ASN ILE THR ALA ILE ILE ALA GLU TYR LYS SEQRES 5 A 247 ARG LYS SER PRO SER GLY LEU ASP VAL GLU ARG ASP PRO SEQRES 6 A 247 ILE GLU TYR SER LYS PHE MET GLU ARG TYR ALA VAL GLY SEQRES 7 A 247 LEU SER ILE LEU THR GLU GLU LYS TYR PHE ASN GLY SER SEQRES 8 A 247 TYR GLU THR LEU ARG LYS ILE ALA SER SER VAL SER ILE SEQRES 9 A 247 PRO ILE LEU MET LYS ASP PHE ILE VAL LYS GLU SER GLN SEQRES 10 A 247 ILE ASP ASP ALA TYR ASN LEU GLY ALA ASP THR VAL LEU SEQRES 11 A 247 LEU ILE VAL LYS ILE LEU THR GLU ARG GLU LEU GLU SER SEQRES 12 A 247 LEU LEU GLU TYR ALA ARG SER TYR GLY MET GLU PRO LEU SEQRES 13 A 247 ILE GLU ILE ASN ASP GLU ASN ASP LEU ASP ILE ALA LEU SEQRES 14 A 247 ARG ILE GLY ALA ARG PHE ILE GLY ILE ASN SER ARG ASP SEQRES 15 A 247 LEU GLU THR LEU GLU ILE ASN LYS GLU ASN GLN ARG LYS SEQRES 16 A 247 LEU ILE SER MET ILE PRO SER ASN VAL VAL LYS VAL ALA SEQRES 17 A 247 GLU SER GLY ILE SER GLU ARG ASN GLU ILE GLU GLU LEU SEQRES 18 A 247 ARG LYS LEU GLY VAL ASN ALA PHE LEU ILE GLY SER SER SEQRES 19 A 247 LEU MET ARG ASN PRO GLU LYS ILE LYS GLU PHE ILE LEU HET IGP A 300 19 HETNAM IGP INDOLE-3-GLYCEROL PHOSPHATE FORMUL 2 IGP C11 H14 N O6 P FORMUL 3 HOH *242(H2 O) HELIX 1 1 GLY A 7 LEU A 17 1 11 HELIX 2 2 LEU A 33 LYS A 42 1 10 HELIX 3 3 PRO A 66 ARG A 75 1 10 HELIX 4 4 TYR A 93 SER A 102 1 10 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 19 GLU A 51 LYS A 53 PHE A 89 LYS A 110 SITE 2 AC1 19 PHE A 112 LEU A 131 GLU A 159 ASN A 180 SITE 3 AC1 19 GLU A 210 SER A 211 GLY A 212 LEU A 231 SITE 4 AC1 19 GLY A 233 SER A 234 HOH A 901 HOH A 902 SITE 5 AC1 19 HOH A1078 HOH A1171 HOH A1317 CRYST1 57.900 73.800 104.200 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 0.017271 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013550 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009597 0.00000