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Yorodumi- PDB-3feu: Crystal Structure of DsbA-like thioredoxin domain VF_A0457 from V... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3feu | ||||||
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Title | Crystal Structure of DsbA-like thioredoxin domain VF_A0457 from Vibrio fischeri | ||||||
Components | putative Lipoprotein | ||||||
Keywords | OXIDOREDUCTASE / alpha-beta structure / Structural Genomics / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG / Lipoprotein / unknown function | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Vibrio fischeri (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.758 Å | ||||||
Authors | Kim, Y. / Sather, A. / Shackelford, G. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) | ||||||
Citation | Journal: To be Published Title: Crystal Structure of DsbA-like thioredoxin domain VF_A0457 from Vibrio fischeri Authors: Kim, Y. / Sather, A. / Shackelford, G. / Joachimiak, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3feu.cif.gz | 55.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3feu.ent.gz | 41 KB | Display | PDB format |
PDBx/mmJSON format | 3feu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3feu_validation.pdf.gz | 431.6 KB | Display | wwPDB validaton report |
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Full document | 3feu_full_validation.pdf.gz | 433.9 KB | Display | |
Data in XML | 3feu_validation.xml.gz | 11.3 KB | Display | |
Data in CIF | 3feu_validation.cif.gz | 16 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fe/3feu ftp://data.pdbj.org/pub/pdb/validation_reports/fe/3feu | 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: 20781.918 Da / Num. of mol.: 1 / Fragment: residues 30-211 Source method: isolated from a genetically manipulated source Details: N-terminal 6-His tag with TEV protease cleavage site Source: (gene. exp.) Vibrio fischeri (bacteria) / Strain: ES114 / Gene: VF_A0457 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21DE3 / References: UniProt: Q5E0B9 |
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#2: Chemical | ChemComp-MG / |
#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 Å3/Da / Density % sol: 38.62 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 0.2 M Sodium chloride, 0.1 M BIS-TRIS pH 5.5, 25 % w/v Polyehtlyene glycol 3,350, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9793 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 22, 2008 / Details: mirrors |
Radiation | Monochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→41.59 Å / Num. all: 17131 / Num. obs: 17131 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.9 % / Biso Wilson estimate: 26.75 Å2 / Rmerge(I) obs: 0.118 / Net I/σ(I): 9.5 |
Reflection shell | Resolution: 1.75→1.78 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.584 / Mean I/σ(I) obs: 2.05 / Num. unique all: 768 / % possible all: 90.8 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.758→41.59 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.942 / SU B: 8.699 / SU ML: 0.119 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.148 / ESU R Free: 0.143 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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: 19.103 Å2
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Refinement step | Cycle: LAST / Resolution: 1.758→41.59 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.758→1.803 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 44.5185 Å / Origin y: 45.2287 Å / Origin z: 7.6555 Å
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