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Open data
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Basic information
Entry | Database: PDB / ID: 4h63 | ||||||
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Title | Structure of the Schizosaccharomyces pombe Mediator head module | ||||||
![]() | (Mediator of RNA polymerase II transcription subunit ...) x 6 | ||||||
![]() | TRANSCRIPTION / MEDIATOR COMPLEX / NUCLEUS | ||||||
Function / homology | ![]() core mediator complex / mediator complex / termination of RNA polymerase II transcription / positive regulation of transcription initiation by RNA polymerase II / transcription initiation at RNA polymerase II promoter / transcription coregulator activity / transcription coactivator activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / regulation of transcription by RNA polymerase II / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Lariviere, L. / Plaschka, C. / Seizl, M. / Wenzeck, L. / Kurth, F. / Cramer, P. | ||||||
![]() | ![]() Title: Structure of the Mediator head module. Authors: Lariviere, L. / Plaschka, C. / Seizl, M. / Wenzeck, L. / Kurth, F. / Cramer, P. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 479.6 KB | Display | ![]() |
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PDB format | ![]() | 399.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 482.6 KB | Display | ![]() |
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Full document | ![]() | 518.4 KB | Display | |
Data in XML | ![]() | 40.2 KB | Display | |
Data in CIF | ![]() | 55 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related 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
-Mediator of RNA polymerase II transcription subunit ... , 6 types, 6 molecules FHKQRV
#1: Protein | Mass: 21163.836 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: 972h / Gene: med6, pmc5, SPAC1002.15c / Production host: ![]() ![]() |
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#2: Protein | Mass: 23360.068 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: 972h / Gene: med8, sep15, SPBC21.04 / Production host: ![]() ![]() |
#3: Protein | Mass: 12644.226 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: 972h / Gene: med11, SPAC644.10 / Production host: ![]() ![]() |
#4: Protein | Mass: 53877.922 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: 972h / Gene: med17, SPBC31F10.04c, srb4 / Production host: ![]() ![]() |
#5: Protein | Mass: 24214.533 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: 972h / Gene: med18, pmc6, sep11, SPAC5D6.05 / Production host: ![]() ![]() |
#6: Protein | Mass: 15264.969 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: 972h / Gene: med22, SPAC29A4.07, srb6 / Production host: ![]() ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.91 Å3/Da / Density % sol: 74.96 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 50 mM MES, 1 M ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 293K, pH 6.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Apr 2, 2012 / Details: mirrors |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.99977 Å / Relative weight: 1 |
Reflection | Resolution: 3.4→126.093 Å / Num. all: 41454 / Num. obs: 41454 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10 % / Biso Wilson estimate: 82.19 Å2 / Rmerge(I) obs: 0.125 / Rsym value: 0.125 / Net I/σ(I): 15.16 |
Reflection shell | Resolution: 3.4→3.49 Å / Redundancy: 9.2 % / Rmerge(I) obs: 0.04124 / Mean I/σ(I) obs: 0.64 / Num. unique all: 3007 / Rsym value: 0.04124 / % possible all: 99.9 |
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Processing
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Refinement | Method to determine structure: ![]()
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Displacement parameters | Biso mean: 165.62 Å2
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Refine analyze | Luzzati coordinate error obs: 1.139 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.4→126.093 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.4→3.49 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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