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- PDB-1jul: INDOLE-3-GLYCEROLPHOSPHATE SYNTHASE FROM SULFOLOBUS SOLFATARICUS ... -

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Basic information

Entry
Database: PDB / ID: 1jul
TitleINDOLE-3-GLYCEROLPHOSPHATE SYNTHASE FROM SULFOLOBUS SOLFATARICUS IN A SECOND ORTHORHOMBIC CRYSTAL FORM
ComponentsINDOLE-3-GLYCEROL PHOSPHATE SYNTHASE
KeywordsLYASE / THERMOPHILE / TIM-BARREL / TRYPTOPHAN BIOSYNTHESIS
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 synthase
Similarity search - Component
Biological speciesSulfolobus solfataricus (archaea)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsKnoechel, T.R. / Hennig, M. / Merz, A. / Darimont, B. / Kirschner, K. / Jansonius, J.N.
Citation
Journal: J.Mol.Biol. / Year: 1996
Title: The crystal structure of indole-3-glycerol phosphate synthase from the hyperthermophilic archaeon Sulfolobus solfataricus in three different crystal forms: effects of ionic strength.
Authors: Knochel, T.R. / Hennig, M. / Merz, A. / Darimont, B. / Kirschner, K. / Jansonius, J.N.
#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
DepositionMay 3, 1996Processing site: BNL
Revision 1.0Jul 7, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 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-GLYCEROL PHOSPHATE SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,8212
Polymers28,6261
Non-polymers1951
Water4,522251
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)62.600, 74.000, 74.200
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-GLYCEROL PHOSPHATE SYNTHASE / IGPS


Mass: 28626.102 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: SECOND ORTHORHOMBIC CRYSTAL FORM / Source: (gene. exp.) Sulfolobus solfataricus (archaea) / Strain: M4 / Gene: TRPC / Plasmid: PDS SS-1 / Gene (production host): TRPC / Production host: Escherichia coli (E. coli)
References: UniProt: Q06121, indole-3-glycerol-phosphate synthase
#2: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 251 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3 Å3/Da / Density % sol: 60 %
Crystal growpH: 6.5 / Details: pH 6.5
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 %(w/v)PEG80001reservoir
28 %(v/v)etylene glycol1reservoir
30.1 MMES1reservoir

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceWavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 5, 1995
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→13.4 Å / Num. obs: 27656 / % possible obs: 99.5 % / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Rmerge(I) obs: 0.078 / Net I/σ(I): 7.8
Reflection shellResolution: 2→2.06 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.256 / Mean I/σ(I) obs: 2.9 / % possible all: 100
Reflection shell
*PLUS
% possible obs: 100 %

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Processing

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

1igs


Resolution: 2→12 Å / σ(F): 0
RfactorNum. reflection% reflection
Rwork0.176 --
obs0.176 23719 99.8 %
Displacement parametersBiso mean: 19.9 Å2
Refinement stepCycle: LAST / Resolution: 2→12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2003 0 12 251 2266
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.009
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_deg1.92
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
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS

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