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- PDB-1vc4: Crystal Structure of Indole-3-Glycerol Phosphate Synthase (TrpC) ... -

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Basic information

Entry
Database: PDB / ID: 1vc4
TitleCrystal Structure of Indole-3-Glycerol Phosphate Synthase (TrpC) from Thermus Thermophilus At 1.8 A Resolution
ComponentsIndole-3-Glycerol Phosphate Synthase
KeywordsLYASE / Tryptophan Biosynthesis / RIKEN Structural Genomics/Proteomics Initiative / RSGI / Structural Genomics
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 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
ACETIC ACID / indole-3-glycerol-phosphate synthase
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsBagautdinov, B. / Tahirov, T.H. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2011
Title: Structure of indole-3-glycerol phosphate synthase from Thermus thermophilus HB8: implications for thermal stability.
Authors: Bagautdinov, B. / Yutani, K.
History
DepositionMar 4, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 23, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 29, 2014Group: Database references
Revision 1.4Oct 25, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 / _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)56,26218
Polymers54,9092
Non-polymers1,35316
Water12,304683
1
A: Indole-3-Glycerol Phosphate Synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,0558
Polymers27,4551
Non-polymers6007
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: Indole-3-Glycerol Phosphate Synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,20710
Polymers27,4551
Non-polymers7539
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
B: Indole-3-Glycerol Phosphate Synthase
hetero molecules

A: Indole-3-Glycerol Phosphate Synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,26218
Polymers54,9092
Non-polymers1,35316
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_544-x,y-1/2,-z-1/21
Buried area2740 Å2
ΔGint-142 kcal/mol
Surface area21610 Å2
MethodPISA
4
A: Indole-3-Glycerol Phosphate Synthase
hetero molecules

B: Indole-3-Glycerol Phosphate Synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,26218
Polymers54,9092
Non-polymers1,35316
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x+1/2,-y,z+1/21
Buried area3170 Å2
ΔGint-132 kcal/mol
Surface area21180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.652, 78.193, 91.523
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe biological assembly is a monomer

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Components

#1: Protein Indole-3-Glycerol Phosphate Synthase


Mass: 27454.748 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Gene: TrpC / Plasmid: PET-11A / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P84126, indole-3-glycerol-phosphate synthase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H4O2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 683 / 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: 2.08 Å3/Da / Density % sol: 40.77 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 4.8
Details: Ammonium Sulfate 1.93M, Acet. 0.68, pH 4.8, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-D / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jan 12, 2004 / Details: mirrors
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→33.56 Å / Num. all: 43028 / Num. obs: 42011 / % possible obs: 97.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.23 % / Biso Wilson estimate: 22.1 Å2 / Rmerge(I) obs: 0.074 / Net I/σ(I): 12.6
Reflection shellResolution: 1.8→1.88 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 4.33 / Num. unique all: 5290 / % possible all: 92.5

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
MOLREPphasing
CNS1.1refinement
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1LBF

1lbf


Resolution: 1.8→33.56 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.218 2107 -RANDOM
Rwork0.186 ---
all-43028 --
obs-42011 97.6 %-
Displacement parametersBiso mean: 24.96 Å2
Baniso -1Baniso -2Baniso -3
1--3.8 Å20 Å20 Å2
2---2.59 Å20 Å2
3---6.38 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.21 Å0.17 Å
Luzzati d res low-5 Å
Luzzati sigma a0.17 Å0.14 Å
Refinement stepCycle: LAST / Resolution: 1.8→33.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3864 0 76 683 4623
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d22.8
X-RAY DIFFRACTIONc_improper_angle_d0.86
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkRfactor Rfree errorNum. reflection obs% reflection obs (%)
1.8-1.880.3122450.2750.02489492.5
1.88-1.980.2472740.2080.015510996.3
1.98-2.110.2382810.1890.014520897.6
2.11-2.270.2272610.1890.014523598.2
2.27-2.50.2362570.1790.015528699
2.5-2.860.2262630.1820.014535199.3

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