+Open data
-Basic information
Entry | Database: PDB / ID: 7bmu | ||||||
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Title | p62PH in cesium chloride (0.25 M CsCl in protein buffer) | ||||||
Components | RNA polymerase II transcription factor B 73 kDa subunit-like protein | ||||||
Keywords | TRANSCRIPTION / Cesium / Phasing / Pleckstrin homology domain | ||||||
Function / homology | Function and homology information transcription factor TFIIH core complex / transcription factor TFIIH holo complex / transcription by RNA polymerase I / nucleotide-excision repair / transcription by RNA polymerase II Similarity search - Function | ||||||
Biological species | Chaetomium thermophilum (fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å | ||||||
Authors | Koelmel, W. / Kuper, J. / Kisker, C. | ||||||
Funding support | Germany, 1items
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Citation | Journal: Sci Rep / Year: 2021 Title: Cesium based phasing of macromolecules: a general easy to use approach for solving the phase problem. Authors: Koelmel, W. / Kuper, J. / Kisker, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7bmu.cif.gz | 41.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7bmu.ent.gz | 27.1 KB | Display | PDB format |
PDBx/mmJSON format | 7bmu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7bmu_validation.pdf.gz | 563.8 KB | Display | wwPDB validaton report |
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Full document | 7bmu_full_validation.pdf.gz | 563.9 KB | Display | |
Data in XML | 7bmu_validation.xml.gz | 8.5 KB | Display | |
Data in CIF | 7bmu_validation.cif.gz | 12.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bm/7bmu ftp://data.pdbj.org/pub/pdb/validation_reports/bm/7bmu | HTTPS FTP |
-Related structure data
Related structure data | 7bmoC 7bmpC 7bmqC 7bmrC 7bmsC 7bmtC 7bmvC 7bmwC 7bmxC 7bmyC 7bmzC C: citing same article (ref.) |
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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
#1: Protein | Mass: 15184.287 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus) Strain: DSM 1495 / CBS 144.50 / IMI 039719 / Gene: CTHT_0001260 / Production host: Escherichia coli (E. coli) / References: UniProt: G0RZ08 | ||||||||
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#2: Chemical | #3: Chemical | ChemComp-K / | #4: Chemical | ChemComp-CS / | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.29 Å3/Da / Density % sol: 46.37 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop / Details: 0.8 M potassium chloride, 17 % (w/v) PEG 4000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 1.7712 Å | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 11, 2016 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.7712 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.9→75.9 Å / Num. obs: 11097 / % possible obs: 97.4 % / Redundancy: 21.3 % / CC1/2: 0.999 / Rmerge(I) obs: 0.08 / Rpim(I) all: 0.017 / Rrim(I) all: 0.082 / Net I/σ(I): 28.7 / Num. measured all: 236591 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.9→53.26 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.933 / SU B: 2.902 / SU ML: 0.088 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.132 / ESU R Free: 0.14 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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 max: 91.13 Å2 / Biso mean: 28.638 Å2 / Biso min: 15.57 Å2
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Refinement step | Cycle: final / Resolution: 1.9→53.26 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.949 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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