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Yorodumi- PDB-2ogk: Crystal structure of protein AF2318 from Archaeglobus fulgidus, P... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2ogk | ||||||
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Title | Crystal structure of protein AF2318 from Archaeglobus fulgidus, Pfam DUF54 | ||||||
Components | Hypothetical protein | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / conserved hypothetical protein / Archaeglobus fulgidus / 10077d / PSI-2 / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC | ||||||
Function / homology | Uncharacterised protein family UPF0201 / RNA binding / 50s Ribosomal Protein L5; Chain: A, / Ribosomal protein L5 / Ribosomal protein L5 domain superfamily / 2-Layer Sandwich / Alpha Beta / Uncharacterized protein Function and homology information | ||||||
Biological species | Archaeoglobus fulgidus (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3 Å | ||||||
Authors | Rao, K.N. / Burley, S.K. / Swaminathan, S. / New York SGX Research Center for Structural Genomics (NYSGXRC) | ||||||
Citation | Journal: Plos One / Year: 2008 Title: UPF201 archaeal specific family members reveal structural similarity to RNA-binding proteins but low likelihood for RNA-binding function. Authors: Rao, K.N. / Burley, S.K. / Swaminathan, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2ogk.cif.gz | 115.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ogk.ent.gz | 91 KB | Display | PDB format |
PDBx/mmJSON format | 2ogk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2ogk_validation.pdf.gz | 446.6 KB | Display | wwPDB validaton report |
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Full document | 2ogk_full_validation.pdf.gz | 465.9 KB | Display | |
Data in XML | 2ogk_validation.xml.gz | 23.5 KB | Display | |
Data in CIF | 2ogk_validation.cif.gz | 31.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/og/2ogk ftp://data.pdbj.org/pub/pdb/validation_reports/og/2ogk | HTTPS FTP |
-Related structure data
Related structure data | 2nrqC 2nwuC 2pzzC 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: 16632.053 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Archaeoglobus fulgidus (archaea) / Gene: AF_2318 / Production host: Escherichia coli (E. coli) / References: UniProt: O27966 #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 3.94 Å3/Da / Density % sol: 68.81 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 Details: PEG MME 5000, HEPES Buffer, Tacsimate, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction |
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Diffraction source |
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Detector |
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Radiation |
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Radiation wavelength |
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Reflection | Resolution: 3→50 Å / Num. all: 21971 / Num. obs: 21971 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.6 % / Biso Wilson estimate: 40 Å2 / Rmerge(I) obs: 0.084 / Net I/σ(I): 8.7 | ||||||||||||||||||
Reflection shell | Resolution: 3→3.12 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.446 / Mean I/σ(I) obs: 2.3 / Num. unique all: 2350 / % possible all: 99.1 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 3→46.7 Å / Rfactor Rfree error: 0.015 / Data cutoff high absF: 55130.26 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber Details: Residues listed as missing are due to lack of electron density, and residues for which side chain atoms are missing have been modeled as alanines
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 37.0738 Å2 / ksol: 0.311229 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 63.3 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3→46.7 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3→3.19 Å / Rfactor Rfree error: 0.047 / Total num. of bins used: 6
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Xplor file |
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