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Yorodumi- PDB-4u4p: Crystal structure of the human condensin SMC hinge domain heterod... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4u4p | ||||||
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Title | Crystal structure of the human condensin SMC hinge domain heterodimer with short coiled coils | ||||||
Components |
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Keywords | PROTEIN BINDING / Condensin / SMC | ||||||
Function / homology | Function and homology information condensin complex => GO:0000796 / condensin complex => GO:0000796 / meiotic chromosome condensation / condensin complex / kinetochore organization / meiotic chromosome segregation / mitotic chromosome condensation / Condensation of Prometaphase Chromosomes / nuclear chromosome / mitotic sister chromatid segregation ...condensin complex => GO:0000796 / condensin complex => GO:0000796 / meiotic chromosome condensation / condensin complex / kinetochore organization / meiotic chromosome segregation / mitotic chromosome condensation / Condensation of Prometaphase Chromosomes / nuclear chromosome / mitotic sister chromatid segregation / chromosome, centromeric region / condensed chromosome / Condensation of Prophase Chromosomes / single-stranded DNA binding / nuclear speck / cell division / nucleolus / extracellular exosome / nucleoplasm / ATP binding / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.89 Å | ||||||
Authors | Uchiyama, S. / Kawahara, K. / Hosokawa, Y. / Fukakusa, S. / Oki, H. / Nakamura, S. / Noda, M. / Takino, R. / Miyahara, Y. / Maruno, T. ...Uchiyama, S. / Kawahara, K. / Hosokawa, Y. / Fukakusa, S. / Oki, H. / Nakamura, S. / Noda, M. / Takino, R. / Miyahara, Y. / Maruno, T. / Kobayashi, Y. / Ohkubo, T. / Fukui, K. | ||||||
Citation | Journal: to be published Title: Structural basis for dimer information and DNA recognition of human SMC proteins Authors: Uchiyama, S. / Kawahara, K. / Hosokawa, Y. / Fukakusa, S. / Oki, H. / Nakamura, S. / Noda, M. / Takino, R. / Miyahara, Y. / Maruno, T. / Kobayashi, Y. / Ohkubo, T. / Fukui, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4u4p.cif.gz | 105.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4u4p.ent.gz | 77.8 KB | Display | PDB format |
PDBx/mmJSON format | 4u4p.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4u4p_validation.pdf.gz | 431.3 KB | Display | wwPDB validaton report |
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Full document | 4u4p_full_validation.pdf.gz | 434.2 KB | Display | |
Data in XML | 4u4p_validation.xml.gz | 19.7 KB | Display | |
Data in CIF | 4u4p_validation.cif.gz | 28.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u4/4u4p ftp://data.pdbj.org/pub/pdb/validation_reports/u4/4u4p | HTTPS FTP |
-Related structure data
Related structure data | 3l51S 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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Unit cell |
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-Components
#1: Protein | Mass: 26278.309 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 476-707 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SMC2, CAPE, SMC2L1, PRO0324 / Production host: Escherichia coli (E. coli) / References: UniProt: O95347 |
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#2: Protein | Mass: 27906.041 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 566-809 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SMC4, CAPC, SMC4L1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9NTJ3 |
#3: 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: 2.23 Å3/Da / Density % sol: 44.86 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 0.1M Tris-HCl pH 8.5, 19% PEG 3350, 50mM NaCl |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å | |||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 9, 2011 | |||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 | |||||||||||||||||||||||||||
Reflection | Resolution: 1.89→46.99 Å / Num. obs: 47639 / % possible obs: 98.4 % / Redundancy: 4.4 % / Biso Wilson estimate: 23.43 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.066 / Rpim(I) all: 0.044 / Net I/σ(I): 10.8 / Num. measured all: 209398 / Scaling rejects: 29 | |||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software | Name: PHENIX / Version: 1.9_1692 / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3L51 Resolution: 1.89→45.191 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / Phase error: 22.29 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.89→45.191 Å
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Refine LS restraints |
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LS refinement shell |
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