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Yorodumi- PDB-3i8n: A domain of a conserved functionally known protein from Vibrio pa... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3i8n | ||||||
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Title | A domain of a conserved functionally known protein from Vibrio parahaemolyticus RIMD 2210633. | ||||||
Components | uncharacterized protein VP2912 | ||||||
Keywords | structural genomics / unknown function / APC64273.1 / Vibrio parahaemolyticus RIMD 2210633 / PSI-2 / protein structure initiative / midwest center for structural genomics / MCSG. | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Vibrio parahaemolyticus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.145 Å | ||||||
Authors | Tan, K. / Tesar, C. / Bearden, J. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) | ||||||
Citation | Journal: To be Published Title: A domain of a conserved functionally known protein from Vibrio parahaemolyticus RIMD 2210633. Authors: Tan, K. / Tesar, C. / Bearden, J. / Joachimiak, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3i8n.cif.gz | 112.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3i8n.ent.gz | 93.7 KB | Display | PDB format |
PDBx/mmJSON format | 3i8n.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3i8n_validation.pdf.gz | 454.3 KB | Display | wwPDB validaton report |
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Full document | 3i8n_full_validation.pdf.gz | 462 KB | Display | |
Data in XML | 3i8n_validation.xml.gz | 13.3 KB | Display | |
Data in CIF | 3i8n_validation.cif.gz | 17.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i8/3i8n ftp://data.pdbj.org/pub/pdb/validation_reports/i8/3i8n | 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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2 |
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3 |
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Unit cell |
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Details | Experimentally unknown. The chains A and B may form a dimer. |
-Components
#1: Protein | Mass: 15005.357 Da / Num. of mol.: 2 / Fragment: residues189-315 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vibrio parahaemolyticus (bacteria) / Strain: RIMD 2210633 / Gene: Vibrio parahaemolyticus, VP2912 / Plasmid: pMCSG19 / Production host: Escherichia coli (E. coli) / Strain (production host): pPK1037 / References: UniProt: Q87KR4 #2: Chemical | #3: 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: 2.95 Å3/Da / Density % sol: 58.26 % |
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Crystal grow | Temperature: 297 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 0.1M Bis-Tris Propane 2.0M Sodium Format, pH 7.0, 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: 0.97931 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 27, 2009 / Details: mirror |
Radiation | Monochromator: Si 111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97931 Å / Relative weight: 1 |
Reflection | Resolution: 2.145→50 Å / Num. all: 20653 / Num. obs: 20653 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 15.6 % / Rmerge(I) obs: 0.15 / Net I/σ(I): 45.3 |
Reflection shell | Resolution: 2.15→2.19 Å / Redundancy: 14.3 % / Rmerge(I) obs: 0.736 / Mean I/σ(I) obs: 4.16 / Num. unique all: 1009 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.145→49.036 Å / SU ML: 0.34 / σ(F): 1.89 / σ(I): 0 / Stereochemistry target values: ML Details: The number of reflections listed here treats f+ and f- separately.
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 62.327 Å2 / ksol: 0.354 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.145→49.036 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION
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Refinement TLS params. | Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group | Selection details: chain B |