HEADER LYASE 03-APR-02 1LBF
TITLE CRYSTAL STRUCTURE OF INDOLE-3-GLYCEROL PHOSPHATE SYNTASE (IGPS)WITH
TITLE 2 REDUCED 1-(O-CABOXYPHENYLAMINO)-1-DEOXYRIBULOSE 5-PHOSPHATE (RCDRP)
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: INDOLE-3-GLYCEROL PHOSPHATE SYNTHASE;
COMPND 3 CHAIN: A;
COMPND 4 EC: 4.1.1.48;
COMPND 5 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: SULFOLOBUS SOLFATARICUS;
SOURCE 3 ORGANISM_TAXID: 2287;
SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562
KEYWDS PROTEIN LIGAND COMPLEX, BETA BARREL, TRYPTOPHAN BIOSYNTHESIS,
KEYWDS 2 SUBSTRATE ANALOGUE COMPLEX, LYASE
EXPDTA X-RAY DIFFRACTION
AUTHOR M.HENNIG,B.DARIMONT,K.KIRSCHNER,J.N.JANSONIUS
REVDAT 4 16-AUG-23 1LBF 1 REMARK
REVDAT 3 24-FEB-09 1LBF 1 VERSN
REVDAT 2 01-APR-03 1LBF 1 JRNL
REVDAT 1 12-JUN-02 1LBF 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 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. 2.05 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) : 2.05
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)) : NULL
REMARK 3 COMPLETENESS (WORKING+TEST) (%) : NULL
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) : 0.152
REMARK 3 FREE R VALUE : 0.225
REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL
REMARK 3 FREE R VALUE TEST SET COUNT : 1364
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 : 23
REMARK 3 SOLVENT ATOMS : 253
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : NULL
REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL
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) : 0.013
REMARK 3 BOND ANGLES (DEGREES) : NULL
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 1LBF COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 04-APR-02.
REMARK 100 THE DEPOSITION ID IS D_1000015812.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 10-AUG-95
REMARK 200 TEMPERATURE (KELVIN) : 293
REMARK 200 PH : 5.0
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-20
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 1.54
REMARK 200 MONOCHROMATOR : NULL
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) : 2.050
REMARK 200 RESOLUTION RANGE LOW (A) : 12.000
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 95.7
REMARK 200 DATA REDUNDANCY : NULL
REMARK 200 R MERGE (I) : 0.07000
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.05
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.20
REMARK 200 COMPLETENESS FOR SHELL (%) : 95.0
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 <I/SIGMA(I)> FOR SHELL : NULL
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: FOURIER SYNTHESIS
REMARK 200 SOFTWARE USED: X-PLOR
REMARK 200 STARTING MODEL: 1IGS
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 68.47
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.90
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 30% AMMONIUM SULPHATE, 50 MM PHOSPHATE
REMARK 280 BUFFER, PH 5.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K
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 28.90000
REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000
REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 52.20000
REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 36.85000
REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 52.20000
REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 28.90000
REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 36.85000
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 LYS A 98 NZ
REMARK 480 ARG A 216 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 GLN A 27 -90.15 -79.27
REMARK 500 SER A 211 139.45 83.09
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 137 A 300
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 1IGS RELATED DB: PDB
REMARK 900 APO STRUCTURE OF THE PROTEIN
REMARK 900 RELATED ID: 1A53 RELATED DB: PDB
REMARK 900 CONTAINS THE SAME PROTEIN COMPLEXED WITH INDOLE-3-GLYCEROL PHOSPHATE
REMARK 900 RELATED ID: 1LBL RELATED DB: PDB
REMARK 900 CONTAINS THE SAME PROTEIN COMPLEXED WITH INDOLE-3-GLYCEROL PHOSPHATE
DBREF 1LBF 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 137 A 300 23
HETNAM 137 1-(O-CARBOXY-PHENYLAMINO)-1-DEOXY-D-RIBULOSE-5-
HETNAM 2 137 PHOSPHATE
FORMUL 2 137 C12 H18 N O9 P
FORMUL 3 HOH *253(H2 O)
HELIX 1 1 LYS A 6 ARG A 18 1 13
HELIX 2 2 SER A 32 ARG A 43 1 12
HELIX 3 3 ASP A 65 GLU A 74 1 10
HELIX 4 4 SER A 92 VAL A 103 1 12
HELIX 5 5 LYS A 115 GLY A 126 1 12
HELIX 6 6 LYS A 135 LEU A 137 5 3
HELIX 7 7 THR A 138 SER A 151 1 14
HELIX 8 8 ASP A 162 ILE A 172 1 11
HELIX 9 9 ASN A 190 ILE A 201 1 12
HELIX 10 10 GLU A 215 LEU A 225 1 11
HELIX 11 11 GLY A 233 ASN A 239 1 7
HELIX 12 12 GLU A 241 ILE A 247 1 7
SHEET 1 A 9 ILE A 48 TYR A 52 0
SHEET 2 A 9 GLY A 79 LEU A 83 1 O SER A 81 N TYR A 52
SHEET 3 A 9 ILE A 107 LYS A 110 1 O LEU A 108 N LEU A 80
SHEET 4 A 9 THR A 129 ILE A 133 1 O THR A 129 N MET A 109
SHEET 5 A 9 LEU A 157 ILE A 160 1 O GLU A 159 N LEU A 132
SHEET 6 A 9 PHE A 176 ASN A 180 1 O GLY A 178 N ILE A 160
SHEET 7 A 9 VAL A 206 GLU A 210 1 O VAL A 208 N ILE A 179
SHEET 8 A 9 ALA A 229 ILE A 232 1 O LEU A 231 N ALA A 209
SHEET 9 A 9 ILE A 48 TYR A 52 1 N ILE A 49 O PHE A 230
SITE 1 AC1 24 TRP A 8 GLU A 51 LYS A 53 SER A 56
SITE 2 AC1 24 PRO A 57 SER A 58 PHE A 89 LYS A 110
SITE 3 AC1 24 ARG A 182 LEU A 184 LEU A 187 GLU A 210
SITE 4 AC1 24 SER A 211 GLY A 212 LEU A 231 GLY A 233
SITE 5 AC1 24 SER A 234 HOH A 901 HOH A 902 HOH A1078
SITE 6 AC1 24 HOH A1171 HOH A1316 HOH A1318 HOH A1320
CRYST1 57.800 73.700 104.400 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 0.017301 0.000000 0.000000 0.00000
SCALE2 0.000000 0.013569 0.000000 0.00000
SCALE3 0.000000 0.000000 0.009579 0.00000
(ATOM LINES ARE NOT SHOWN.)
END
