+Open data
-Basic information
Entry | Database: PDB / ID: 2qry | ||||||
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Title | Periplasmic thiamin binding protein | ||||||
Components | Thiamine-binding periplasmic protein | ||||||
Keywords | TRANSPORT PROTEIN / thiamin binding protein / periplasmic / ABC transporter | ||||||
Function / homology | Function and homology information thiamine binding / thiamine transport / thiamine pyrophosphate binding / transmembrane transport / outer membrane-bounded periplasmic space Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.25 Å | ||||||
Authors | Ealick, S.E. / Soriano, E.V. | ||||||
Citation | Journal: Biochemistry / Year: 2008 Title: Structural Similarities between Thiamin-Binding Protein and Thiaminase-I Suggest a Common Ancestor Authors: Soriano, E.V. / Rajashankar, K.R. / Hanes, J.W. / Bale, S. / Begley, T.P. / Ealick, S.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2qry.cif.gz | 254.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2qry.ent.gz | 215.3 KB | Display | PDB format |
PDBx/mmJSON format | 2qry.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qr/2qry ftp://data.pdbj.org/pub/pdb/validation_reports/qr/2qry | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 36824.621 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: thiB, tbpA / Production host: Escherichia coli (E. coli) / References: UniProt: P31550 #2: Chemical | ChemComp-TPS / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.49 Å3/Da / Density % sol: 50.68 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.2 Details: 2.0 M (NH4)2SO4, 0.1 M Na citrate, and 0.2 M Na/K tartrate, pH 5.2, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: CHESS / Beamline: F2 / Wavelength: 0.9795 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: May 26, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.25→49.39 Å / Num. all: 124110 / Num. obs: 61739 / % possible obs: 89.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.3 % / Biso Wilson estimate: 22.8 Å2 / Rmerge(I) obs: 0.115 / Rsym value: 0.115 / Net I/σ(I): 11.8 |
Reflection shell | Resolution: 2.25→2.39 Å / Redundancy: 2 % / Mean I/σ(I) obs: 2.7 / Rsym value: 0.386 / % possible all: 81.1 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.25→49.39 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 2574069.29 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 37.4622 Å2 / ksol: 0.4 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.25→49.39 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.25→2.39 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
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Xplor file |
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