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- PDB-1i4n: CRYSTAL STRUCTURE OF INDOLEGLYCEROL PHOSPHATE SYNTHASE FROM THERM... -

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Basic information

Entry
Database: PDB / ID: 1i4n
TitleCRYSTAL STRUCTURE OF INDOLEGLYCEROL PHOSPHATE SYNTHASE FROM THERMOTOGA MARITIMA
ComponentsINDOLE-3-GLYCEROL PHOSPHATE SYNTHASE
KeywordsLYASE / Indoleglycerol phosphate synthase / Thermotoga maritima / Thermostable TIM-barrel protein / Salt bridges / Electrostatic interactions
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 speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsKnoechel, T. / Pappenberger, A. / Jansonius, J.N. / Kirschner, K.
CitationJournal: J.Biol.Chem. / Year: 2002
Title: The crystal structure of indoleglycerol-phosphate synthase from Thermotoga maritima. Kinetic stabilization by salt bridges.
Authors: Knochel, T. / Pappenberger, A. / Jansonius, J.N. / Kirschner, K.
History
DepositionFeb 22, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 20, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: INDOLE-3-GLYCEROL PHOSPHATE SYNTHASE
B: INDOLE-3-GLYCEROL PHOSPHATE SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,3344
Polymers57,1422
Non-polymers1922
Water1,44180
1
A: INDOLE-3-GLYCEROL PHOSPHATE SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,6672
Polymers28,5711
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: INDOLE-3-GLYCEROL PHOSPHATE SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,6672
Polymers28,5711
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.930, 48.930, 248.040
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

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Components

#1: Protein INDOLE-3-GLYCEROL PHOSPHATE SYNTHASE / INDOLEGLYCEROL PHOSPHATE SYNTHASE / IGPS


Mass: 28571.000 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Production host: Escherichia coli (E. coli)
References: UniProt: Q56319, indole-3-glycerol-phosphate synthase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 80 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.6 Å3/Da / Density % sol: 52.64 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6
Details: PEG 8000, ammonium phosphate, cacodylate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 7.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
113 mg/mlprotein1drop
22 mMEDTA1drop
31 mM1,4-DTT1drop
410 mMpotassium phosphate1droppH7.5
58-11 %(w/v)PEG80001reservoir
6160-180 mMammonium sulfate1reservoir
7100 mMsodium cacodylate1reservoirpH6.0

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM1A / Wavelength: 0.8722 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 12, 1996
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8722 Å / Relative weight: 1
ReflectionResolution: 2.47→30 Å / Num. all: 20875 / Num. obs: 20875 / % possible obs: 99.7 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 5.8 % / Biso Wilson estimate: 44.6 Å2 / Rmerge(I) obs: 0.064 / Net I/σ(I): 6.7
Reflection shellResolution: 2.47→2.53 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.202 / Mean I/σ(I) obs: 3.6 / % possible all: 96.2
Reflection
*PLUS
Reflection shell
*PLUS
% possible obs: 96.2 %

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
TRUNCATEdata reduction
AMoREphasing
X-PLOR3.1refinement
CCP4(TRUNCATE)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→30 Å / σ(F): 1 / σ(I): 1 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.233 2372 RANDOM
Rwork0.169 --
all0.172 19968 -
obs0.172 19968 -
Refinement stepCycle: LAST / Resolution: 2.5→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4020 0 10 80 4110
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.011
X-RAY DIFFRACTIONx_angle_deg1.625
Refinement
*PLUS
σ(F): 1 / % reflection Rfree: 5 % / Rfactor obs: 0.169
Solvent computation
*PLUS
Displacement parameters
*PLUS

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