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- PDB-1wv2: Crystal structure of thiamine biosynthesis protein from Pseudomon... -

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Basic information

Entry
Database: PDB / ID: 1wv2
TitleCrystal structure of thiamine biosynthesis protein from Pseudomonas Aeruginosa
ComponentsThiazole biosynthesis protein thiG
KeywordsBIOSYNTHETIC PROTEIN / Structural genomics / PROTEIN STRUCTURE INITIATIVE / PSI / New York SGX Research Center for Structural Genomics / NYSGXRC target T1779 / thiamine biosynthesis / TIM barrel
Function / homology
Function and homology information


thiazole synthase / sulfurtransferase activity / thiamine diphosphate biosynthetic process / thiamine biosynthetic process / cytoplasm
Similarity search - Function
Thiazole synthase / Thiazole synthase ThiG / Thiazole biosynthesis protein ThiG / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.9 Å
AuthorsFedorov, A.A. / Fedorov, E.V. / Almo, S.C. / Burley, S.K. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Crystal structure of thiamine biosynthesis protein from Pseudomonas Aeruginosa
Authors: Fedorov, A.A. / Fedorov, E.V. / Almo, S.C.
History
DepositionDec 10, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 21, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2017Group: Database references / Category: pdbx_database_related
Revision 1.4Feb 3, 2021Group: Structure summary / Category: audit_author / Item: _audit_author.identifier_ORCID
Revision 1.5Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Thiazole biosynthesis protein thiG
B: Thiazole biosynthesis protein thiG


Theoretical massNumber of molelcules
Total (without water)56,5252
Polymers56,5252
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1760 Å2
ΔGint-14 kcal/mol
Surface area20230 Å2
MethodPISA
2
A: Thiazole biosynthesis protein thiG
B: Thiazole biosynthesis protein thiG

A: Thiazole biosynthesis protein thiG
B: Thiazole biosynthesis protein thiG


Theoretical massNumber of molelcules
Total (without water)113,0514
Polymers113,0514
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_556-x,-x+y,-z+4/31
Buried area9480 Å2
ΔGint-87 kcal/mol
Surface area34500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.115, 74.115, 164.947
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Thiazole biosynthesis protein thiG / thiazole moeity


Mass: 28262.658 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: Q9I6B4

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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: 2.21 Å3/Da / Density % sol: 42.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 4.5
Details: Sodium Chloride, Sodium acetate, pH 4.5, VAPOR DIFFUSION, temperature 293.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X9A / Wavelength: 0.979, 0.97934, 0.97911, 0.97166
DetectorType: MARRESEARCH / Detector: CCD / Date: Sep 26, 2004
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9791
20.979341
30.979111
40.971661
ReflectionResolution: 2.9→25 Å / Num. all: 11974 / Num. obs: 11974 / % possible obs: 98.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.9→3 Å / % possible all: 97.1

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
CNS1refinement
RefinementMethod to determine structure: MAD / Resolution: 2.9→25 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.304 611 RANDOM
Rwork0.254 --
all0.257 11974 -
obs0.257 11974 -
Refinement stepCycle: LAST / Resolution: 2.9→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3384 0 0 0 3384
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.4

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