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- PDB-1a53: COMPLEX OF INDOLE-3-GLYCEROLPHOSPHATE SYNTHASE FROM SULFOLOBUS SO... -

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Basic information

Entry
Database: PDB / ID: 1a53
TitleCOMPLEX OF INDOLE-3-GLYCEROLPHOSPHATE SYNTHASE FROM SULFOLOBUS SOLFATARICUS WITH INDOLE-3-GLYCEROLPHOSPHATE AT 2.0 A RESOLUTION
ComponentsINDOLE-3-GLYCEROLPHOSPHATE SYNTHASE
KeywordsSYNTHASE / THERMOSTABLE / TIM-BARREL
Function / homology
Function and homology information


indole-3-glycerol-phosphate synthase / indole-3-glycerol-phosphate synthase activity / phosphoribosylanthranilate isomerase activity / L-tryptophan biosynthetic process
Similarity search - Function
Indole-3-glycerol phosphate synthase, conserved site / Indole-3-glycerol phosphate synthase signature. / Indole-3-glycerol phosphate synthase domain / Indole-3-glycerol phosphate synthase / Indole-3-glycerol phosphate synthase / Ribulose-phosphate binding barrel / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
INDOLE-3-GLYCEROL PHOSPHATE / Indole-3-glycerol phosphate synthase
Similarity search - Component
Biological speciesSulfolobus solfataricus (archaea)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsHennig, M. / Darimont, B. / Kirschner, K. / Jansonius, J.N.
Citation
Journal: J.Mol.Biol. / Year: 2002
Title: The catalytic mechanism of indole-3-glycerol phosphate synthase: crystal structures of complexes of the enzyme from Sulfolobus solfataricus with substrate analogue, substrate, and product.
Authors: Hennig, M. / Darimont, B.D. / Jansonius, J.N. / Kirschner, K.
#1: Journal: Structure / Year: 1995
Title: 2.0 A Structure of Indole-3-Glycerol Phosphate Synthase from the Hyperthermophile Sulfolobus Solfataricus: Possible Determinants of Protein Stability
Authors: Hennig, M. / Darimont, B. / Sterner, R. / Kirschner, K. / Jansonius, J.N.
History
DepositionFeb 19, 1998Processing site: BNL
Revision 1.0Mar 23, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 2, 2023Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Refinement description
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: INDOLE-3-GLYCEROLPHOSPHATE SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,7822
Polymers28,4951
Non-polymers2871
Water4,360242
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.900, 73.800, 104.200
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein INDOLE-3-GLYCEROLPHOSPHATE SYNTHASE / IGPS


Mass: 28494.906 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus solfataricus (archaea) / Gene: TRPC / Plasmid: REPRESSOR PLASMID PDM / Species (production host): Escherichia coli / Gene (production host): TRPC
Production host: Escherichia coli str. K12 substr. W3110 (bacteria)
Strain (production host): W3110
References: UniProt: Q06121, indole-3-glycerol-phosphate synthase
#2: Chemical ChemComp-IGP / INDOLE-3-GLYCEROL PHOSPHATE


Mass: 287.206 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H14NO6P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 242 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.91 Å3/Da / Density % sol: 68.5 %
Crystal growpH: 5.5 / Details: pH 5.5
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
120 mg/mlenzyme1drop
226-30 %satammonium sulfate1drop
326-30 %satammonium sulfate1reservoir

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: ROTATING ANODE / Type: ELLIOTT GX-21 / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 10, 1994
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→15 Å / Num. obs: 27283 / % possible obs: 91.1 % / Observed criterion σ(I): 0 / Redundancy: 5.1 % / Biso Wilson estimate: 32.2 Å2 / Rmerge(I) obs: 0.063 / Net I/σ(I): 10
Reflection shellResolution: 2→2.05 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 1.6 / Rsym value: 0.39 / % possible all: 48
Reflection
*PLUS
Num. obs: 28014 / Num. measured all: 141730

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1IGS

1igs


Resolution: 2→15 Å / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.212 -10 %RANDOM
Rwork0.159 ---
obs0.159 27283 91.1 %-
Displacement parametersBiso mean: 29.6 Å2
Refinement stepCycle: LAST / Resolution: 2→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2003 0 19 242 2264
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.012
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.7
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 2→2.07 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.3527 88 10 %
Rwork0.303 1705 -
obs--48 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARAM19X.PROTOPH19X.PRO
X-RAY DIFFRACTION2PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION3IGP.PRXIGP.TPX

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