+Open data
-Basic information
Entry | Database: PDB / ID: 2ojh | ||||||
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Title | The structure of putative TolB from Agrobacterium tumefaciens | ||||||
Components | Uncharacterized protein Atu1656/AGR_C_3050 | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / tolB / Agrobacterium tumefaciens / 6-stranded beta-propeller / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG | ||||||
Function / homology | WD40-like beta propeller / WD40-like Beta Propeller Repeat / TolB, C-terminal domain / Six-bladed beta-propeller, TolB-like / 6 Propeller / Neuraminidase / Mainly Beta / ACETIC ACID / Uncharacterized protein Atu1656 Function and homology information | ||||||
Biological species | Agrobacterium tumefaciens str. (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.85 Å | ||||||
Authors | Cuff, M.E. / Xu, X. / Gu, J. / Edwards, A. / Savchenko, A. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) | ||||||
Citation | Journal: TO BE PUBLISHED Title: The structure of putative TolB from Agrobacterium tumefaciens Authors: Cuff, M.E. / Xu, X. / Gu, J. / Edwards, A. / Savchenko, A. / Joachimiak, A. | ||||||
History |
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Remark 300 | BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 ... BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN(S). AUTHORS STATE THAT THE BIOLOGICAL UNIT OF THIS PROTEIN IS UNKNOWN AT THE TIME OF DEPOSITION. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2ojh.cif.gz | 79.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ojh.ent.gz | 58.5 KB | Display | PDB format |
PDBx/mmJSON format | 2ojh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2ojh_validation.pdf.gz | 434.5 KB | Display | wwPDB validaton report |
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Full document | 2ojh_full_validation.pdf.gz | 435.8 KB | Display | |
Data in XML | 2ojh_validation.xml.gz | 16 KB | Display | |
Data in CIF | 2ojh_validation.cif.gz | 24.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oj/2ojh ftp://data.pdbj.org/pub/pdb/validation_reports/oj/2ojh | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 33666.812 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Agrobacterium tumefaciens str. (bacteria) Species: Agrobacterium tumefaciens / Strain: C58 / Gene: tolB / Plasmid: p11 variant / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q8UEU8 | ||
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#2: Chemical | #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.77 Å3/Da / Density % sol: 55.65 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.1M Sodium cacodylate pH 6.5, 0.2M Magnesium acetate, 20% PEG 8000, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97918, 0.97935 | |||||||||
Detector | Type: CUSTOM-MADE / Detector: CCD / Date: Jun 3, 2006 | |||||||||
Radiation | Monochromator: SAGITALLY FOCUSED Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||
Radiation wavelength |
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Reflection | Resolution: 1.85→35.5 Å / Num. all: 29685 / Num. obs: 29685 / % possible obs: 93.8 % / Observed criterion σ(I): -3 / Redundancy: 6.5 % / Biso Wilson estimate: 24.3 Å2 / Rsym value: 0.087 / Net I/σ(I): 9.7 | |||||||||
Reflection shell | Resolution: 1.85→1.89 Å / Redundancy: 5.1 % / Mean I/σ(I) obs: 3.4 / Rsym value: 0.335 / % possible all: 70.1 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.85→35.5 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.944 / SU B: 5.954 / SU ML: 0.091 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.127 / ESU R Free: 0.127 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 39.757 Å2
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Refinement step | Cycle: LAST / Resolution: 1.85→35.5 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.85→1.898 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 13.8034 Å / Origin y: 44.6815 Å / Origin z: 15.2 Å
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