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Yorodumi- PDB-2e6u: Crystal structure of hypothetical protein PH1109 from Pyrococcus ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2e6u | |||||||||
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Title | Crystal structure of hypothetical protein PH1109 from Pyrococcus horikoshii | |||||||||
Components | hypothetical protein PH1109 | |||||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / Rossmann-like / CoA binding / Structural Genomics Consortium for Research on Gene Expression System | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | Pyrococcus horikoshii (archaea) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å | |||||||||
Authors | Kitago, Y. / Min, Y. / Watanabe, N. / Tanaka, I. | |||||||||
Citation | Journal: ACTA CRYSTALLOGR.,SECT.D / Year: 2005 Title: Structure determination of a novel protein by sulfur SAD using chromium radiation in combination with a new crystal-mounting method Authors: Kitago, Y. / Watanabe, N. / Tanaka, I. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2e6u.cif.gz | 45.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2e6u.ent.gz | 31.4 KB | Display | PDB format |
PDBx/mmJSON format | 2e6u.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2e6u_validation.pdf.gz | 688.9 KB | Display | wwPDB validaton report |
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Full document | 2e6u_full_validation.pdf.gz | 689.8 KB | Display | |
Data in XML | 2e6u_validation.xml.gz | 8.6 KB | Display | |
Data in CIF | 2e6u_validation.cif.gz | 10.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e6/2e6u ftp://data.pdbj.org/pub/pdb/validation_reports/e6/2e6u | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 16747.432 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Strain: OT3 / Gene: PH1109 / Plasmid: pET-26b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O58836 | ||||
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#2: Chemical | ChemComp-CA / | ||||
#3: Chemical | #4: Chemical | ChemComp-COA / | #5: 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: 2.97 Å3/Da / Density % sol: 58.62 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 40% (v/v) PEG 300, 0.1M Cacodylate buffer pH6.5, 0.2M Calcium acetate, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 24, 2004 / Details: mirrors |
Radiation | Monochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→50 Å / Num. all: 19648 / Num. obs: 19648 / % possible obs: 100 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 13.6 % / Biso Wilson estimate: 21.426 Å2 / Rsym value: 0.073 / Net I/σ(I): 23.3 |
Reflection shell | Resolution: 1.8→1.86 Å / Redundancy: 12.8 % / Mean I/σ(I) obs: 6.6 / Num. unique all: 1905 / Rsym value: 0.458 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.8→20 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.928 / SU B: 1.934 / SU ML: 0.062 / Cross valid method: THROUGHOUT / ESU R: 0.114 / ESU R Free: 0.111 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.373 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.8→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.802→1.848 Å / Total num. of bins used: 20
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