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Yorodumi- PDB-6m2m: A role for histone chaperone OsChz1 in histone recognition and de... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6m2m | ||||||
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Title | A role for histone chaperone OsChz1 in histone recognition and deposition | ||||||
Components |
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Keywords | CHAPERONE / complex | ||||||
Function / homology | Function and homology information heterochromatin formation => GO:0031507 / chloroplast / structural constituent of chromatin / nucleosome / protein heterodimerization activity / DNA binding / extracellular region / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Arabidopsis thaliana (thale cress) Oryza sativa subsp. japonica (Japanese rice) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.85 Å | ||||||
Authors | Luo, Q. / Wang, B. | ||||||
Citation | Journal: Nat Commun / Year: 2020 Title: OsChz1 acts as a histone chaperone in modulating chromatin organization and genome function in rice. Authors: Du, K. / Luo, Q. / Yin, L. / Wu, J. / Liu, Y. / Gan, J. / Dong, A. / Shen, W.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6m2m.cif.gz | 212.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6m2m.ent.gz | 168.8 KB | Display | PDB format |
PDBx/mmJSON format | 6m2m.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m2/6m2m ftp://data.pdbj.org/pub/pdb/validation_reports/m2/6m2m | 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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Unit cell |
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-Components
#1: Protein | Mass: 10049.619 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: At4g27230, M4I22.40 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O81826 #2: Protein | Mass: 11033.928 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: At1g07790, F24B9.10 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9LQQ4 #3: Protein | Mass: 11448.044 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Oryza sativa subsp. japonica (Japanese rice) Gene: LOC_Os11g34190, Os11g0544600, OSNPB_110544600 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q2R2Z3 #4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | N | |
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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: 2.8 Å3/Da / Density % sol: 56.02 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 0.2M Sodium citrate,0.1M Tris-HCl pH 8.5, 30%(w/v) |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97915 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: May 31, 2017 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97915 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.85→30 Å / Num. obs: 41445 / % possible obs: 99.2 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.098 / Rpim(I) all: 0.063 / Rrim(I) all: 0.117 / Χ2: 0.887 / Net I/σ(I): 7.5 / Num. measured all: 134001 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.85→30 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.903 / SU B: 15.064 / SU ML: 0.284 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.81 / ESU R Free: 0.352 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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 max: 165.6 Å2 / Biso mean: 60.24 Å2 / Biso min: 1.32 Å2
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Refinement step | Cycle: final / Resolution: 2.85→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.85→2.923 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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