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Yorodumi- PDB-3eur: Crystal structure of the C-terminal domain of uncharacterized pro... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3eur | ||||||
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Title | Crystal structure of the C-terminal domain of uncharacterized protein from Bacteroides fragilis NCTC 9343 | ||||||
Components | uncharacterized protein | ||||||
Keywords | structural genomics / unknown function / PSI2 / MCSG / conserved protein / Protein Structure Initiative / Midwest Center for Structural Genomics | ||||||
Function / homology | Function and homology information Domain of unknown function DUF5106 / Domain of unknown function (DUF5106) / Thioredoxin-like / Thioredoxin-like fold / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta Similarity search - Domain/homology | ||||||
Biological species | Bacteroides fragilis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.3 Å | ||||||
Authors | Nocek, B. / Tesar, C. / Cobb, G. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) | ||||||
Citation | Journal: To be Published Title: Crystal structure of the C-terminal domain of uncharacterized protein from Bacteroides fragilis NCTC 9343 Authors: Nocek, B. / Tesar, C. / Cobb, 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 | 3eur.cif.gz | 81.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3eur.ent.gz | 61.7 KB | Display | PDB format |
PDBx/mmJSON format | 3eur.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3eur_validation.pdf.gz | 427.5 KB | Display | wwPDB validaton report |
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Full document | 3eur_full_validation.pdf.gz | 430.7 KB | Display | |
Data in XML | 3eur_validation.xml.gz | 10.4 KB | Display | |
Data in CIF | 3eur_validation.cif.gz | 15.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/eu/3eur ftp://data.pdbj.org/pub/pdb/validation_reports/eu/3eur | 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: 16245.474 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacteroides fragilis (bacteria) / Strain: NCTC 9343 / Gene: BF1587 / Plasmid: pMCSG19 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21DE(3) / References: UniProt: Q5LF10, UniProt: A0A380Z3E8*PLUS |
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#2: 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: 2.19 Å3/Da / Density % sol: 43.74 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.2 M Potassium sodium tartrate tetrahydrate 20% Peg 3350, pH 7.5, 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-BM / Wavelength: 0.9794 Å |
Detector | Type: SBC-3 / Detector: CCD / Date: Sep 30, 2008 / Details: mirror |
Radiation | Monochromator: SI CRYSTAL 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9794 Å / Relative weight: 1 |
Reflection | Resolution: 1.3→50 Å / Num. all: 35647 / Num. obs: 32763 / % possible obs: 91.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 8 % / Rmerge(I) obs: 0.043 / Net I/σ(I): 44.7 |
Reflection shell | Resolution: 1.3→1.334 Å / Redundancy: 4 % / Rmerge(I) obs: 0.15 / Mean I/σ(I) obs: 5.14 / Num. unique all: 884 / % possible all: 50 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.3→49.33 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.963 / SU B: 1.152 / SU ML: 0.023 / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / ESU R: 0.053 / ESU R Free: 0.05 / 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: 12.084 Å2
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Refinement step | Cycle: LAST / Resolution: 1.3→49.33 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.3→1.334 Å / Total num. of bins used: 20
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