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Yorodumi- PDB-2e8f: Crystal Structure of a hypothetical protein (Aq_1549) from Aquife... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2e8f | ||||||
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Title | Crystal Structure of a hypothetical protein (Aq_1549) from Aquifex aeolicus VF5 (Oxidised form) | ||||||
Components | Hypothetical protein Aq_1549 | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / hypothetical protein / Aq_1549 / Osmatically induced protein / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | OsmC/Ohr family / OsmC/Ohr superfamily / OsmC-like protein / K homology (KH) domain / GMP Synthetase; Chain A, domain 3 / K homology domain-like, alpha/beta / 2-Layer Sandwich / Alpha Beta / OsmC family peroxiredoxin Function and homology information | ||||||
Biological species | Aquifex aeolicus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Kumarevel, T.S. / Kuramitsu, S. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: To be Published Title: Crystal Structure of a hypothetical protein (Aq_1549) from Aquifex aeolicus VF5 Authors: Kumarevel, T.S. / Kuramitsu, S. / Yokoyama, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2e8f.cif.gz | 40.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2e8f.ent.gz | 27.2 KB | Display | PDB format |
PDBx/mmJSON format | 2e8f.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2e8f_validation.pdf.gz | 420.4 KB | Display | wwPDB validaton report |
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Full document | 2e8f_full_validation.pdf.gz | 422.3 KB | Display | |
Data in XML | 2e8f_validation.xml.gz | 8.1 KB | Display | |
Data in CIF | 2e8f_validation.cif.gz | 10.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e8/2e8f ftp://data.pdbj.org/pub/pdb/validation_reports/e8/2e8f | HTTPS FTP |
-Related structure data
Related structure data | 2e8eC 2e8cS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | |
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: 15037.618 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aquifex aeolicus (bacteria) / Strain: VF5 / Plasmid: pET21a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)Codonplus-RIL-X / References: UniProt: O67503 |
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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: 2.14 Å3/Da / Density % sol: 42.5 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 50% PEG 200, 0.1M Citrate, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Sep 26, 2006 / Details: Si |
Radiation | Monochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→40 Å / Num. all: 12327 / Num. obs: 12327 / % possible obs: 97.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 13.8 % / Biso Wilson estimate: 18.7 Å2 / Rmerge(I) obs: 0.061 |
Reflection shell | Resolution: 1.8→1.86 Å / Redundancy: 13.9 % / Rmerge(I) obs: 0.339 / Num. unique all: 1177 / % possible all: 96 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2E8C Resolution: 1.8→19.58 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 1231571.25 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 65.8602 Å2 / ksol: 0.40037 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.8→19.58 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.91 Å / Rfactor Rfree error: 0.024 / Total num. of bins used: 6
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Xplor file |
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