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Yorodumi- PDB-3eop: Crystal Structure of the DUF55 domain of human thymocyte nuclear ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3eop | ||||||
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Title | Crystal Structure of the DUF55 domain of human thymocyte nuclear protein 1 | ||||||
Components | Thymocyte nuclear protein 1 | ||||||
Keywords | UNKNOWN FUNCTION / Nucleus / Phosphoprotein | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3 Å | ||||||
Authors | Yu, F. / Song, A. / Xu, C. / Sun, L. / Li, L. / Tang, L. / Hu, H. / He, J. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2009 Title: Determining the DUF55-domain structure of human thymocyte nuclear protein 1 from crystals partially twinned by tetartohedry Authors: Yu, F. / Song, A. / Xu, C. / Sun, L. / Li, J. / Tang, L. / Yu, M. / Yeates, T.O. / Hu, H. / He, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3eop.cif.gz | 81.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3eop.ent.gz | 60.7 KB | Display | PDB format |
PDBx/mmJSON format | 3eop.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3eop_validation.pdf.gz | 447.5 KB | Display | wwPDB validaton report |
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Full document | 3eop_full_validation.pdf.gz | 460.7 KB | Display | |
Data in XML | 3eop_validation.xml.gz | 16.1 KB | Display | |
Data in CIF | 3eop_validation.cif.gz | 20.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/eo/3eop ftp://data.pdbj.org/pub/pdb/validation_reports/eo/3eop | HTTPS FTP |
-Related structure data
Related structure data | 2ar1S S: Starting model for refinement |
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Similar structure data |
-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: 20770.738 Da / Num. of mol.: 2 / Fragment: DUF55 domain, UNP residues 55-221 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET22 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3) pLysS / References: UniProt: Q9P016 #2: Chemical | ChemComp-SO4 / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.23 Å3/Da / Density % sol: 44.96 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 10.9 Details: 0.1M NaAc (pH 4.0-4.8), 28% PEG 2000 MME, 200mM (NH4)2SO4, 3% 1,6-diaminohexane as additive, pH 10.9, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: BSRF / Beamline: 3W1A / Wavelength: 1 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Mar 7, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→44.41 Å / Num. all: 15997 / Num. obs: 15931 / % possible obs: 99.4 % / Redundancy: 4.8 % / Biso Wilson estimate: 40.06 Å2 / Rmerge(I) obs: 0.056 |
Reflection shell | Resolution: 2.3→2.42 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.291 / Num. unique all: 2326 / % possible all: 98.8 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 2ar1 Resolution: 2.3→44.39 Å / Occupancy max: 1 / Occupancy min: 1 / Data cutoff high absF: 0 / σ(F): 0 Details: Thin resolution shells. Quadruplets of twin related reflections were kept together in either the test set or the refinement set throughout refinement.
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Solvent computation | Bsol: 59.208 Å2 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 68.11 Å2 / Biso mean: 36.2394 Å2 / Biso min: 5.91 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.3→44.39 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.38 Å
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Xplor file |
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