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- PDB-3cwi: Crystal structure of thiamine biosynthesis protein (ThiS) from Ge... -

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Basic information

Entry
Database: PDB / ID: 3cwi
TitleCrystal structure of thiamine biosynthesis protein (ThiS) from Geobacter metallireducens. Northeast Structural Genomics Consortium Target GmR137
ComponentsThiamine-biosynthesis protein ThiS
KeywordsBIOSYNTHETIC PROTEIN / alpha-beta protein / Structural Genomics / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homology
Function and homology information


ThiS, thiamine-biosynthesis / Sulfur carrier ThiS/MoaD-like / ThiS family / Molybdopterin synthase/thiamin biosynthesis sulphur carrier, beta-grasp / Beta-grasp domain / Beta-grasp domain superfamily / Ubiquitin-like (UB roll) / Roll / Alpha Beta
Similarity search - Domain/homology
Thiamin biosynthesis sulfur carrier protein
Similarity search - Component
Biological speciesGeobacter metallireducens GS-15 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å
AuthorsForouhar, F. / Abashidze, M. / Seetharaman, J. / Mao, L. / Janjua, H. / Xiao, R. / Maglaqui, M. / Ciccosanti, C. / Foote, E.L. / Wang, H. ...Forouhar, F. / Abashidze, M. / Seetharaman, J. / Mao, L. / Janjua, H. / Xiao, R. / Maglaqui, M. / Ciccosanti, C. / Foote, E.L. / Wang, H. / Everett, J.K. / Acton, T.B. / Montelione, G.T. / Tong, L. / Hunt, J.F. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Crystal structure of thiamine biosynthesis protein (ThiS) from Geobacter metallireducens.
Authors: Forouhar, F. / Abashidze, M. / Seetharaman, J. / Mao, L. / Janjua, H. / Xiao, R. / Maglaqui, M. / Ciccosanti, C. / Foote, E.L. / Wang, H. / Everett, J.K. / Acton, T.B. / Montelione, G.T. / Tong, L. / Hunt, J.F.
History
DepositionApr 21, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 6, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 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_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Thiamine-biosynthesis protein ThiS


Theoretical massNumber of molelcules
Total (without water)8,6241
Polymers8,6241
Non-polymers00
Water81145
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)40.965, 40.965, 89.537
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
DetailsAUTHORS STATE THAT THE MONOMERIC ASSEMBLY OF THE BIOLOGICAL UNIT THAT IS SHOWN IN REMARK 350 IS PUTATIVE

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Components

#1: Protein Thiamine-biosynthesis protein ThiS


Mass: 8624.253 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacter metallireducens GS-15 (bacteria)
Species: Geobacter metallireducens / Strain: GS-15 / DSM 7210 / Gene: ThiS, Gmet_1567 / Plasmid: pET21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+Magic / References: UniProt: Q39VC5
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 45 / 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: 2.18 Å3/Da / Density % sol: 43.52 %
Description: The structure factor file contains Friedel pairs
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5
Details: Protein solution: 10 mM Tris-HCl pH 7.5, 100 mM NaCl, 5 mM DTT. Reservoir solution: 100 mM Sodium acetate pH 5.0, 18% PEG 8000, 200 mM Magnesium chloride, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4C / Wavelength: 0.97908 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Apr 2, 2008 / Details: Mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97908 Å / Relative weight: 1
ReflectionResolution: 1.9→30 Å / Num. all: 11436 / Num. obs: 11436 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 14.5 % / Biso Wilson estimate: 16 Å2 / Rmerge(I) obs: 0.078 / Rsym value: 0.063 / Net I/σ(I): 40.74
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 10.8 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 4.54 / Num. unique all: 1152 / Rsym value: 0.328 / % possible all: 99.8

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Processing

Software
NameVersionClassification
CNS1.2refinement
ADSCQuantumdata collection
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.9→19.97 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 856078.58 / Data cutoff low absF: 0 / Isotropic thermal model: OVERALL / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber / Details: The Friedel pairs were used in phasing
RfactorNum. reflection% reflectionSelection details
Rfree0.258 1060 10.2 %RANDOM
Rwork0.226 ---
all0.227 11436 --
obs0.226 10382 90.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 59.014 Å2 / ksol: 0.45 e/Å3
Displacement parametersBiso mean: 32 Å2
Baniso -1Baniso -2Baniso -3
1-4.2 Å20 Å20 Å2
2--4.2 Å20 Å2
3----8.4 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.31 Å0.23 Å
Luzzati d res low-5 Å
Luzzati sigma a0.18 Å0.05 Å
Refinement stepCycle: LAST / Resolution: 1.9→19.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms513 0 0 45 558
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_dihedral_angle_d25.6
X-RAY DIFFRACTIONc_improper_angle_d0.59
LS refinement shellResolution: 1.9→1.97 Å / Rfactor Rfree error: 0.025 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.24 92 11.6 %
Rwork0.219 702 -
obs-702 69.4 %

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