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Yorodumi- PDB-6af0: Structure of Ctr9, Paf1 and Cdc73 ternary complex from Myceliopht... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6af0 | |||||||||
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Title | Structure of Ctr9, Paf1 and Cdc73 ternary complex from Myceliophthora thermophila | |||||||||
Components |
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Keywords | TRANSCRIPTION / Transcription elongation / Paf1 / Ctr9 / Cdc73 / crystal structure | |||||||||
Function / homology | Function and homology information : / Cdc73/Paf1 complex / transcription elongation by RNA polymerase II / regulation of DNA-templated transcription Similarity search - Function | |||||||||
Biological species | Myceliophthora thermophila (fungus) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.88 Å | |||||||||
Authors | Wang, Z. / Deng, P. / Zhou, Y. | |||||||||
Funding support | China, 2items
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Citation | Journal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2018 Title: Transcriptional elongation factor Paf1 core complex adopts a spirally wrapped solenoidal topology. Authors: Deng, P. / Zhou, Y. / Jiang, J. / Li, H. / Tian, W. / Cao, Y. / Qin, Y. / Kim, J. / Roeder, R.G. / Patel, D.J. / Wang, Z. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6af0.cif.gz | 222.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6af0.ent.gz | 173.7 KB | Display | PDB format |
PDBx/mmJSON format | 6af0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6af0_validation.pdf.gz | 450.9 KB | Display | wwPDB validaton report |
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Full document | 6af0_full_validation.pdf.gz | 486.2 KB | Display | |
Data in XML | 6af0_validation.xml.gz | 40 KB | Display | |
Data in CIF | 6af0_validation.cif.gz | 54.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/af/6af0 ftp://data.pdbj.org/pub/pdb/validation_reports/af/6af0 | HTTPS FTP |
-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: 106251.508 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Myceliophthora thermophila (strain ATCC 42464 / BCRC 31852 / DSM 1799) (fungus) Strain: ATCC 42464 / BCRC 31852 / DSM 1799 / Gene: MYCTH_2305158 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: G2QC65 |
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#2: Protein | Mass: 12983.727 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Myceliophthora thermophila (strain ATCC 42464 / BCRC 31852 / DSM 1799) (fungus) Strain: ATCC 42464 / BCRC 31852 / DSM 1799 / Gene: MYCTH_2303763 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: G2QDK9 |
#3: Protein | Mass: 7659.691 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Myceliophthora thermophila (strain ATCC 42464 / BCRC 31852 / DSM 1799) (fungus) Strain: ATCC 42464 / BCRC 31852 / DSM 1799 / Gene: MYCTH_2298931 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: G2Q3X1 |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.94 Å3/Da / Density % sol: 58.09 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.2M potassium phosphate dibasic, 20% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 77 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9789 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 7, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9789 Å / Relative weight: 1 |
Reflection | Resolution: 2.88→118.89 Å / Num. obs: 34480 / % possible obs: 100 % / Redundancy: 10.4 % / Rmerge(I) obs: 0.075 / Net I/σ(I): 24.7 |
Reflection shell | Resolution: 2.9→2.95 Å / Redundancy: 10.3 % / Rmerge(I) obs: 1.23 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 1718 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.88→118.89 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.885 / SU B: 23.517 / SU ML: 0.434 / Cross valid method: THROUGHOUT / ESU R Free: 0.461 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 93.026 Å2
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Refinement step | Cycle: 1 / Resolution: 2.88→118.89 Å
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Refine LS restraints |
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