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- PDB-3ayh: Crystal structure of the C17/25 subcomplex from S. pombe RNA Poly... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3ayh | ||||||
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Title | Crystal structure of the C17/25 subcomplex from S. pombe RNA Polymerase III | ||||||
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![]() | TRANSCRIPTION | ||||||
Function / homology | ![]() RNA Polymerase III Transcription Initiation From Type 1 Promoter / RNA Polymerase III Transcription Initiation From Type 2 Promoter / chromatin => GO:0000785 / transcription initiation at RNA polymerase III promoter / RNA polymerase III complex / DNA-directed 5'-3' RNA polymerase activity / nucleotide binding / DNA binding / nucleus / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Ehara, H. / Sekine, S. / Yokoyama, S. | ||||||
![]() | ![]() Title: Crystal structure of the C17/25 subcomplex from Schizosaccharomyces pombe RNA polymerase III Authors: Ehara, H. / Sekine, S. / Yokoyama, S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 81.1 KB | Display | ![]() |
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PDB format | ![]() | 60.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 448.9 KB | Display | ![]() |
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Full document | ![]() | 452.4 KB | Display | |
Data in XML | ![]() | 15.1 KB | Display | |
Data in CIF | ![]() | 21.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2ckzS S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 15524.620 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: ATCC 38366 / 972 / Gene: rpc17, SPAPB1E7.10 / Plasmid: pET-Duet1 / Production host: ![]() ![]() | ||
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#2: Protein | Mass: 23268.648 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: ATCC 38366 / 972 / Gene: rpc25, SPBC2G5.07c / Plasmid: pET-Duet1 / Production host: ![]() ![]() | ||
#3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.53 Å3/Da / Density % sol: 51.4 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 1.3M Li2SO4, 0.1M Tris-HCl, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction source | Source: ![]() ![]() ![]() |
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Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: May 31, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.19→34.38 Å / Num. all: 20649 / Num. obs: 20649 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.7 % / Rmerge(I) obs: 0.108 / Net I/σ(I): 6.837 |
Reflection shell | Resolution: 2.19→2.25 Å / Redundancy: 10 % / Rmerge(I) obs: 0.669 / Mean I/σ(I) obs: 4 / Num. unique all: 1524 / % possible all: 99.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2CKZ Resolution: 2.193→34.376 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8599 / SU ML: 0.25 / σ(F): 0 / Phase error: 20.79 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 36.241 Å2 / ksol: 0.373 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 109.72 Å2 / Biso mean: 36.3408 Å2 / Biso min: 12.94 Å2
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Refinement step | Cycle: LAST / Resolution: 2.193→34.376 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7
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