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Yorodumi- PDB-3f9u: Crystal structure of C-terminal domain of putative exported cytoc... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3f9u | ||||||
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Title | Crystal structure of C-terminal domain of putative exported cytochrome C biogenesis-related protein from Bacteroides fragilis | ||||||
Components | Putative exported cytochrome C biogenesis-related protein | ||||||
Keywords | structural genomics / unknown function / exported cytochrome C biogenesis-related protein / Bacteroides fragilis / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG | ||||||
Function / homology | Function and homology information protein-disulfide reductase (NAD(P)H) activity / cytochrome complex assembly / membrane => GO:0016020 Similarity search - Function | ||||||
Biological species | Bacteroides fragilis NCTC 9343 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 Å | ||||||
Authors | Chang, C. / Tesar, C. / Cobb, G. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) | ||||||
Citation | Journal: To be Published Title: Crystal structure of C-terminal domain of putative exported cytochrome C biogenesis-related protein from Bacteroides fragilis Authors: Chang, C. / 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 | 3f9u.cif.gz | 80.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3f9u.ent.gz | 61.2 KB | Display | PDB format |
PDBx/mmJSON format | 3f9u.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3f9u_validation.pdf.gz | 463.3 KB | Display | wwPDB validaton report |
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Full document | 3f9u_full_validation.pdf.gz | 465.4 KB | Display | |
Data in XML | 3f9u_validation.xml.gz | 15.6 KB | Display | |
Data in CIF | 3f9u_validation.cif.gz | 22 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f9/3f9u ftp://data.pdbj.org/pub/pdb/validation_reports/f9/3f9u | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 19984.770 Da / Num. of mol.: 2 / Fragment: C-terminal domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacteroides fragilis NCTC 9343 (bacteria) Strain: strain ATCC 25285 / NCTC 9343 / Gene: BF3033 / Plasmid: pMCSG19 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) derivative / References: UniProt: Q5LAZ4 #2: Chemical | ChemComp-NO3 / #3: Chemical | #4: 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: 2.34 Å3/Da / Density % sol: 47.38 % |
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Crystal grow | Temperature: 297 K / Method: vapor diffusion, sitting drop / pH: 6.9 Details: 0.2 M Potassium nitrate 20% PEG3350, pH 6.9, VAPOR DIFFUSION, SITTING DROP, temperature 297K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97934 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 16, 2008 |
Radiation | Monochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97934 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→50 Å / Num. all: 20114 / Num. obs: 20107 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 11.6 % / Biso Wilson estimate: 36 Å2 / Rmerge(I) obs: 0.126 / Net I/σ(I): 29.49 |
Reflection shell | Resolution: 2.2→2.22 Å / Redundancy: 11.4 % / Rmerge(I) obs: 0.877 / Mean I/σ(I) obs: 3 / Num. unique all: 469 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.2→50 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.93 / SU B: 10.873 / SU ML: 0.126 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.228 / ESU R Free: 0.198 / 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: 26.88 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.201→2.258 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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