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Yorodumi- PDB-3lja: Using Soft X-Rays for a Detailed Picture of Divalent Metal Bindin... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3lja | ||||||
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Title | Using Soft X-Rays for a Detailed Picture of Divalent Metal Binding in the Nucleosome | ||||||
Components |
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Keywords | STRUCTURAL PROTEIN/DNA / Nucleosome / Divalent metal / Cation binding / Counterion / Compaction / Chromosomal protein / DNA-binding / Methylation / Nucleosome core / Nucleus / STRUCTURAL PROTEIN-DNA complex | ||||||
Function / homology | Function and homology information structural constituent of chromatin / nucleosome / nucleosome assembly / protein heterodimerization activity / DNA binding / nucleoplasm / nucleus Similarity search - Function | ||||||
Biological species | Xenopus laevis (African clawed frog) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å | ||||||
Authors | Wu, B. / Davey, C.A. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2010 Title: Using soft X-rays for a detailed picture of divalent metal binding in the nucleosome Authors: Wu, B. / Davey, C.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3lja.cif.gz | 326.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3lja.ent.gz | 247.5 KB | Display | PDB format |
PDBx/mmJSON format | 3lja.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3lja_validation.pdf.gz | 527.3 KB | Display | wwPDB validaton report |
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Full document | 3lja_full_validation.pdf.gz | 549.1 KB | Display | |
Data in XML | 3lja_validation.xml.gz | 35.7 KB | Display | |
Data in CIF | 3lja_validation.cif.gz | 51.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lj/3lja ftp://data.pdbj.org/pub/pdb/validation_reports/lj/3lja | HTTPS FTP |
-Related structure data
Related structure data | 1kx5S S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
-Protein , 4 types, 8 molecules AEBFCGDH
#1: Protein | Mass: 15303.930 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Xenopus laevis (African clawed frog) / Production host: Escherichia coli (E. coli) / References: UniProt: P84233 #2: Protein | Mass: 11263.231 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Xenopus laevis (African clawed frog) / Production host: Escherichia coli (E. coli) / References: UniProt: P62799 #3: Protein | Mass: 13978.241 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Xenopus laevis (African clawed frog) / Gene: LOC494591 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6AZJ8, UniProt: P06897*PLUS #4: Protein | Mass: 13524.752 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Xenopus laevis (African clawed frog) / Production host: Escherichia coli (E. coli) / References: UniProt: P02281 |
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-DNA chain , 2 types, 2 molecules IJ
#5: DNA chain | Mass: 45368.051 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: sequence based on human alpha-satellite DNA |
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#6: DNA chain | Mass: 45359.035 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: sequence based on human alpha-satellite DNA |
-Non-polymers , 2 types, 48 molecules
#7: Chemical | #8: Chemical | ChemComp-MN / |
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-Details
Sequence details | 1. RESIDUES CHAIN A/E ALA 102 COULD BE TREATED AS UNINTENTIONAL MUTATIONS OR VARIATIONS IN GENOMIC ...1. RESIDUES CHAIN A/E ALA 102 COULD BE TREATED AS UNINTENTIO |
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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: 2.68 Å3/Da / Density % sol: 54.06 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 85 mM MnCl2, 60 mM KCl, 20 mM K-Cacodylate, 4 mg/ml NCP over well with 1/2 conc., pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K, EVAPORATION |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.89 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 11, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.89 Å / Relative weight: 1 |
Reflection | Resolution: 2.75→76.5 Å / Num. obs: 53707 / % possible obs: 95.8 % / Redundancy: 6.8 % / Rmerge(I) obs: 0.085 / Net I/σ(I): 21.2 |
Reflection shell | Resolution: 2.75→2.9 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.425 / Mean I/σ(I) obs: 3.6 / Num. unique all: 7216 / % possible all: 89.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1KX5 Resolution: 2.75→38.19 Å / Cor.coef. Fo:Fc: 0.919 / Cor.coef. Fo:Fc free: 0.882 / Cross valid method: THROUGHOUT / ESU R: 1.149 / ESU R Free: 0.352 / 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: 54.531 Å2
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Refinement step | Cycle: LAST / Resolution: 2.75→38.19 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.75→2.821 Å / Total num. of bins used: 20
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