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Yorodumi- PDB-2e8g: The structure of protein from P. horikoshii at 1.7 angstrom resolution -
+Open data
-Basic information
Entry | Database: PDB / ID: 2e8g | ||||||
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Title | The structure of protein from P. horikoshii at 1.7 angstrom resolution | ||||||
Components | Hypothetical protein PH0536Hypothesis | ||||||
Keywords | RNA BINDING PROTEIN / oligonucleotide/oligosaccharide-binding fold / alpha-helices bundle / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Pyrococcus horikoshii (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.7 Å | ||||||
Authors | Gao, Y.G. / Yao, M. / Tanaka, I. | ||||||
Citation | Journal: Proteins / Year: 2008 Title: Structure of protein PH0536 from Pyrococcus horikoshii at 1.7 A resolution reveals a novel assembly of an oligonucleotide/oligosaccharide-binding fold and an alpha-helical bundle Authors: Gao, Y.-G. / Yao, M. / Tanaka, I. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2e8g.cif.gz | 109.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2e8g.ent.gz | 86.2 KB | Display | PDB format |
PDBx/mmJSON format | 2e8g.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e8/2e8g ftp://data.pdbj.org/pub/pdb/validation_reports/e8/2e8g | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 26957.156 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Strain: OT3 / Gene: ph0536 / Plasmid: pET-26b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: O58271 #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: 2.25 Å3/Da / Density % sol: 45.31 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.8 Details: 18% PEG 6000, 5% Glycerol, 0.1M MES, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-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: 1.7→34.401 Å / Num. all: 52501 / Num. obs: 52434 / % possible obs: 99.7 % / Observed criterion σ(F): -1 / Observed criterion σ(I): -1 / Redundancy: 4.3 % / Biso Wilson estimate: 22.656 Å2 / Rmerge(I) obs: 0.049 / Rsym value: 0.049 / Net I/σ(I): 19.7 | ||||||||||||||||||
Reflection shell | Resolution: 1.7→1.76 Å / Redundancy: 4 % / Rmerge(I) obs: 0.353 / Mean I/σ(I) obs: 2.9 / Num. unique all: 5184 / Rsym value: 0.353 / % possible all: 99.3 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.7→34.4 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 21.983 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.7→34.4 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.744 Å / Rfactor Rfree error: 0
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