+Open data
-Basic information
Entry | Database: PDB / ID: 4s3h | ||||||
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Title | Crystal structure of S. pombe Mdb1 FHA domain | ||||||
Components | Mdb1 | ||||||
Keywords | UNKNOWN FUNCTION / Mdb1 / forkhead-associated domain (FHA domain) / dimerization | ||||||
Function / homology | Function and homology information mitotic spindle midzone / mitotic G2 DNA damage checkpoint signaling / site of double-strand break / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Schizosaccharomyces pombe 972h- (yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.701 Å | ||||||
Authors | Luo, S. / Ye, K. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2015 Title: Dimerization Mediated by a Divergent Forkhead-associated Domain Is Essential for the DNA Damage and Spindle Functions of Fission Yeast Mdb1. Authors: Luo, S. / Xin, X. / Du, L.L. / Ye, K. / Wei, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4s3h.cif.gz | 85.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4s3h.ent.gz | 65.5 KB | Display | PDB format |
PDBx/mmJSON format | 4s3h.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/s3/4s3h ftp://data.pdbj.org/pub/pdb/validation_reports/s3/4s3h | 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: 14323.102 Da / Num. of mol.: 4 / Fragment: FHA domain, UNP residues 1-104 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Schizosaccharomyces pombe 972h- (yeast) Strain: 972 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O14079 #2: Chemical | #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: 2.35 Å3/Da / Density % sol: 47.56 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.2 Details: 0.1 M sodium acetate, pH 5.2, 1.8 M ammonium sulfate, vapor diffusion, hanging drop, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: BSRF / Beamline: 3W1A / Wavelength: 1 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Detector: CCD / Date: Mar 11, 2008 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.7→20 Å / Num. obs: 15871 / % possible obs: 99.9 % / Redundancy: 9.6 % / Rmerge(I) obs: 0.102 / Χ2: 0.947 / Net I/σ(I): 7.2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.701→19.759 Å / SU ML: 0.31 / σ(F): 1.35 / Phase error: 25.22 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 128.38 Å2 / Biso mean: 51.9339 Å2 / Biso min: 22.42 Å2 | ||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.701→19.759 Å
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