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Yorodumi- PDB-3jr7: The crystal structure of the protein of DegV family COG1307 with ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3jr7 | ||||||
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Title | The crystal structure of the protein of DegV family COG1307 with unknown function from Ruminococcus gnavus ATCC 29149 | ||||||
Components | uncharacterized egV family protein COG1307 | ||||||
Keywords | structural genomics / unknown function / DegV family / PSI2 / MCSG / Protein Structure Initiative / Midwest Center for Structural Genomics | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Ruminococcus gnavus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å | ||||||
Authors | Zhang, R. / Hatzos, C. / Clancy, S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) | ||||||
Citation | Journal: To be Published Title: The crystal structure of the protein of DegV family COG1307 with unknown function from Ruminococcus gnavus ATCC 29149 Authors: Zhang, R. / Hatzos, C. / Clancy, S. / Joachimiak, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3jr7.cif.gz | 238.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3jr7.ent.gz | 203.6 KB | Display | PDB format |
PDBx/mmJSON format | 3jr7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3jr7_validation.pdf.gz | 801.1 KB | Display | wwPDB validaton report |
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Full document | 3jr7_full_validation.pdf.gz | 809.6 KB | Display | |
Data in XML | 3jr7_validation.xml.gz | 29.5 KB | Display | |
Data in CIF | 3jr7_validation.cif.gz | 43.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jr/3jr7 ftp://data.pdbj.org/pub/pdb/validation_reports/jr/3jr7 | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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Details | This protein exists as monomer. |
-Components
#1: Protein | Mass: 33634.137 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Ruminococcus gnavus (bacteria) / Strain: ATCC 29149 / Gene: RUMGNA_03254 / Plasmid: pMCSG19 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: A7B6P0 #2: Chemical | #3: Chemical | #4: Chemical | ChemComp-NA / #5: 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: 3.22 Å3/Da / Density % sol: 61.82 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 4.2 Details: 0.2M Sodium chloride, 0.1M Phosphate-citrate, 10%PEG3000, pH 4.2, VAPOR DIFFUSION, SITTING DROP, temperature 289K |
-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: Oct 4, 2008 / Details: mirrors |
Radiation | Monochromator: Si 111 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9794 Å / Relative weight: 1 |
Reflection | Resolution: 2→83.92 Å / Num. all: 56152 / Num. obs: 55821 / % possible obs: 99.41 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5.2 % / Rmerge(I) obs: 0.077 / Net I/σ(I): 17.85 |
Reflection shell | Resolution: 2→2.055 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.352 / Mean I/σ(I) obs: 2.1 / Num. unique all: 4365 / % possible all: 99.52 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2→83.92 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.939 / SU B: 5.929 / SU ML: 0.076 / Cross valid method: THROUGHOUT / σ(I): 0 / ESU R: 0.218 / ESU R Free: 0.127 / 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: 22.259 Å2
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Refinement step | Cycle: LAST / Resolution: 2→83.92 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.003→2.055 Å / Total num. of bins used: 20
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