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Yorodumi- PDB-7bmy: p62PH in cesium chloride (0.7 M CsCl in crystallization condition... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7bmy | ||||||
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Title | p62PH in cesium chloride (0.7 M CsCl in crystallization condition and cryo protectant) | ||||||
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 / nucleotide-excision repair / DNA-templated transcription Similarity search - Function | ||||||
Biological species | Chaetomium thermophilum (fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 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 | 7bmy.cif.gz | 40.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7bmy.ent.gz | 29.1 KB | Display | PDB format |
PDBx/mmJSON format | 7bmy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bm/7bmy ftp://data.pdbj.org/pub/pdb/validation_reports/bm/7bmy | HTTPS FTP |
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-Related structure data
Related structure data | 7bmoC 7bmpC 7bmqC 7bmrC 7bmsC 7bmtC 7bmuC 7bmvC 7bmwC 7bmxC 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 on special symmetry positions |
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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 | ChemComp-CS / #3: Chemical | ChemComp-CL / #4: 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: 2.3 Å3/Da / Density % sol: 46.43 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop / Details: 0.7 M cesium chloride, 18 % (w/v) PEG 4000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.77114 Å | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 24, 2014 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.77114 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.8→43.67 Å / Num. obs: 12670 / % possible obs: 94.9 % / Redundancy: 33 % / CC1/2: 0.999 / Rmerge(I) obs: 0.15 / Rpim(I) all: 0.026 / Rrim(I) all: 0.152 / Net I/σ(I): 22 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.8→43.67 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.934 / SU B: 2.318 / SU ML: 0.074 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.13 / ESU R Free: 0.121 / 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: 65.88 Å2 / Biso mean: 19.978 Å2 / Biso min: 8.73 Å2
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Refinement step | Cycle: final / Resolution: 1.8→43.67 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.847 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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