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Yorodumi- PDB-7tkv: Crystal Structure of the Thioredox_DsbH Domain-Containing Unchara... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7tkv | ||||||
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Title | Crystal Structure of the Thioredox_DsbH Domain-Containing Uncharacterized Protein Bab1_2064 from Brucella abortus | ||||||
Components | Thioredox_DsbH domain-containing protein | ||||||
Keywords | UNKNOWN FUNCTION / TRX domain / protein of unkown function / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID | ||||||
Function / homology | Domain of unknown function DUF255 / Spermatogenesis-associated protein 20 / Protein of unknown function, DUF255 / Six-hairpin glycosidase-like superfamily / Six-hairpin glycosidase superfamily / Thioredoxin-like superfamily / carbohydrate metabolic process / PHOSPHATE ION / Thioredox_DsbH domain-containing protein Function and homology information | ||||||
Biological species | Brucella abortus 2308 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.8 Å | ||||||
Authors | Kim, Y. / Crawford, M. / Endres, M. / Babnigg, G. / Crosson, S. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||
Funding support | United States, 1items
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Citation | Journal: To Be Published Title: Crystal Structure of the Thioredox_DsbH Domain-Containing Uncharacterized Protein Bab1_2064 from Brucella abortus Authors: Kim, Y. / Crawford, M. / Endres, M. / Babnigg, G. / Crosson, S. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7tkv.cif.gz | 604.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7tkv.ent.gz | 432.9 KB | Display | PDB format |
PDBx/mmJSON format | 7tkv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tk/7tkv ftp://data.pdbj.org/pub/pdb/validation_reports/tk/7tkv | HTTPS FTP |
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-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: 75339.438 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Brucella abortus 2308 (bacteria) / Strain: 2308 / Gene: BAB1_2064 / Plasmid: pMCSG68 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Gold / References: UniProt: Q2YR10 #2: Chemical | #3: Chemical | ChemComp-PO4 / #4: Chemical | ChemComp-CL / | #5: Water | ChemComp-HOH / | Has ligand of interest | N | |
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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: 2.43 Å3/Da / Density % sol: 49.43 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5.6 / Details: 1.0 M sodium-potassium phosphate pH 5.6 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97929 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 12, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97929 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→50 Å / Num. obs: 35972 / % possible obs: 95.5 % / Redundancy: 5.5 % / Biso Wilson estimate: 62.43 Å2 / CC1/2: 0.992 / Rmerge(I) obs: 0.17 / Net I/σ(I): 10.3 |
Reflection shell | Resolution: 2.8→2.85 Å / Redundancy: 5.4 % / Rmerge(I) obs: 1.181 / Mean I/σ(I) obs: 1.22 / Num. unique obs: 1622 / CC1/2: 0.402 / % possible all: 87.8 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.8→47.25 Å / SU ML: 0.3541 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.3655 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 70.14 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.8→47.25 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group | Refine-ID: X-RAY DIFFRACTION
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