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Yorodumi- PDB-1id3: CRYSTAL STRUCTURE OF THE YEAST NUCLEOSOME CORE PARTICLE REVEALS F... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1id3 | ||||||
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Title | CRYSTAL STRUCTURE OF THE YEAST NUCLEOSOME CORE PARTICLE REVEALS FUNDAMENTAL DIFFERENCES IN INTER-NUCLEOSOME INTERACTIONS | ||||||
Components |
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Keywords | STRUCTURAL PROTEIN/DNA / Nucleosome Core Particle / Chromatin / Histone / Protein/DNA Interaction / Nucleoprotein / Supercoiled DNA / Complex (Nucleosome Core-DNA) / STRUCTURAL PROTEIN-DNA COMPLEX | ||||||
Function / homology | Function and homology information sexual sporulation resulting in formation of a cellular spore / HDMs demethylate histones / HATs acetylate histones / Condensation of Prophase Chromosomes / global genome nucleotide-excision repair / RNA polymerase I upstream activating factor complex / SUMOylation of chromatin organization proteins / replication fork protection complex / RMTs methylate histone arginines / positive regulation of transcription by RNA polymerase I ...sexual sporulation resulting in formation of a cellular spore / HDMs demethylate histones / HATs acetylate histones / Condensation of Prophase Chromosomes / global genome nucleotide-excision repair / RNA polymerase I upstream activating factor complex / SUMOylation of chromatin organization proteins / replication fork protection complex / RMTs methylate histone arginines / positive regulation of transcription by RNA polymerase I / nucleolar large rRNA transcription by RNA polymerase I / rRNA transcription / CENP-A containing nucleosome / nucleosome assembly / structural constituent of chromatin / nucleosome / chromatin organization / protein heterodimerization activity / DNA repair / regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / DNA binding / nucleus Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å | ||||||
Authors | White, C.L. / Suto, R.K. / Luger, K. | ||||||
Citation | Journal: EMBO J. / Year: 2001 Title: Structure of the yeast nucleosome core particle reveals fundamental changes in internucleosome interactions. Authors: White, C.L. / Suto, R.K. / Luger, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1id3.cif.gz | 291.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1id3.ent.gz | 224.4 KB | Display | PDB format |
PDBx/mmJSON format | 1id3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/id/1id3 ftp://data.pdbj.org/pub/pdb/validation_reports/id/1id3 | HTTPS FTP |
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-Related structure data
Related structure data | 1aoiS 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
-DNA chain , 1 types, 2 molecules IJ
#1: DNA chain | Mass: 45054.844 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ALPHA SAT DNA / Plasmid: PUC / Production host: Escherichia coli (E. coli) / Strain (production host): HB101 |
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-Protein , 4 types, 8 molecules AEBFCGDH
#2: Protein | Mass: 15273.836 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: HISTONE H3 / Plasmid: PET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 PLYSS / References: UniProt: P61830 #3: Protein | Mass: 11264.194 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: HISTONE H4 / Plasmid: PET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 PLYSS / References: UniProt: P02309 #4: Protein | Mass: 13881.980 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: HISTONE H2A / Plasmid: PET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 PLYSS / References: UniProt: P04911 #5: Protein | Mass: 14133.145 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: HISTONE H2B / Plasmid: PET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 PLYSS / References: UniProt: P02294 |
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-Non-polymers , 2 types, 77 molecules
#6: Chemical | ChemComp-MN / #7: 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: 2.8 Å3/Da / Density % sol: 56.07 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, sitting drop / pH: 6 Details: Manganese chloride, Potassium chloride, cacodylate, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 292K | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1.1 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 30, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 3.1→40 Å / Num. all: 517812 / Num. obs: 39551 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 13.1 % / Rmerge(I) obs: 0.056 / Net I/σ(I): 14.8 |
Reflection shell | Resolution: 3.1→3.15 Å / Rmerge(I) obs: 0.299 / Mean I/σ(I) obs: 2.17 / % possible all: 99.9 |
Reflection | *PLUS Lowest resolution: 40 Å / Num. measured all: 517812 |
Reflection shell | *PLUS % possible obs: 99.9 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1AOI Resolution: 3.1→40 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 3.1→40 Å
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Refine LS restraints |
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Software | *PLUS Name: CNS / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 3.1 Å / Lowest resolution: 40 Å / σ(F): 0 / Rfactor obs: 0.223 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS |