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Yorodumi- PDB-2e8c: Crystal structure of a hypothetical protein (Aq_1549) from Aquife... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2e8c | ||||||
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Title | Crystal structure of a hypothetical protein (Aq_1549) from Aquifex aeolicus VF5 | ||||||
Components | Hypothetical protein Aq_1549Hypothesis | ||||||
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 / MAD / Resolution: 2.1 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 | 2e8c.cif.gz | 35 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2e8c.ent.gz | 26.7 KB | Display | PDB format |
PDBx/mmJSON format | 2e8c.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e8/2e8c ftp://data.pdbj.org/pub/pdb/validation_reports/e8/2e8c | HTTPS FTP |
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-Related structure data
Related structure data | |
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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: 2.13 Å3/Da / Density % sol: 42.18 % |
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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: BL26B2 / Wavelength: 0.97882, 0.97945, 0.90 | ||||||||||||
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 14, 2006 / Details: Si | ||||||||||||
Radiation | Monochromator: Si / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2.04→46.29 Å / Num. all: 8738 / Num. obs: 8728 / % possible obs: 99.9 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 13.04 % / Biso Wilson estimate: 13.7 Å2 / Rmerge(I) obs: 0.084 | ||||||||||||
Reflection shell | Resolution: 2.04→2.11 Å / Redundancy: 13.48 % / Rmerge(I) obs: 0.336 / Num. unique all: 863 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.1→19.56 Å / Rfactor Rfree error: 0.011 / Data cutoff high absF: 1370738.56 / 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: 70.0738 Å2 / ksol: 0.411596 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.1→19.56 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.23 Å / Rfactor Rfree error: 0.034 / Total num. of bins used: 6
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Xplor file |
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