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Yorodumi- PDB-5umr: Crystal structure of N-terminal domain of human FACT complex subu... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5umr | |||||||||
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Title | Crystal structure of N-terminal domain of human FACT complex subunit SSRP1 | |||||||||
Components | FACT complex subunit SSRP1FACT (biology) | |||||||||
Keywords | TRANSCRIPTION / Histone chaperone / PH domain / human FACT complex | |||||||||
Function / homology | Function and homology information FACT complex / regulation of chromatin organization / nucleosome disassembly / Pausing and recovery of Tat-mediated HIV elongation / Tat-mediated HIV elongation arrest and recovery / HIV elongation arrest and recovery / Pausing and recovery of HIV elongation / nucleosome binding / Tat-mediated elongation of the HIV-1 transcript / Formation of HIV-1 elongation complex containing HIV-1 Tat ...FACT complex / regulation of chromatin organization / nucleosome disassembly / Pausing and recovery of Tat-mediated HIV elongation / Tat-mediated HIV elongation arrest and recovery / HIV elongation arrest and recovery / Pausing and recovery of HIV elongation / nucleosome binding / Tat-mediated elongation of the HIV-1 transcript / Formation of HIV-1 elongation complex containing HIV-1 Tat / Formation of HIV elongation complex in the absence of HIV Tat / RNA Polymerase II Transcription Elongation / Formation of RNA Pol II elongation complex / RNA Polymerase II Pre-transcription Events / TP53 Regulates Transcription of DNA Repair Genes / nucleosome assembly / histone binding / Regulation of TP53 Activity through Phosphorylation / DNA replication / DNA repair / nucleolus / DNA binding / RNA binding / nucleoplasm / nucleus Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.501 Å | |||||||||
Authors | Su, D. / Hu, Q. / Thompson, J.R. / Heroux, A. / Botuyan, M.V. / Mer, G. | |||||||||
Funding support | United States, 2items
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Citation | Journal: To Be Published Title: Crystal structure of N-terminal domain of human FACT complex subunit SSRP1 Authors: Hu, Q. / Su, D. / Thompson, J.R. / Botuyan, M.V. / Mer, G. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5umr.cif.gz | 72.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5umr.ent.gz | 60.1 KB | Display | PDB format |
PDBx/mmJSON format | 5umr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/um/5umr ftp://data.pdbj.org/pub/pdb/validation_reports/um/5umr | HTTPS FTP |
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-Related structure data
Related structure data | |
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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: 12015.189 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SSRP1, FACT80 / Plasmid: pTEV / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q08945 |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.02 Å3/Da / Density % sol: 39.03 % |
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Crystal grow | Temperature: 288 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 2.2 M DL-Malic acid, 100 mM Bis-Tris propane, pH 7.0. |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.979 Å | |||||||||
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 1, 2010 | |||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||
Radiation wavelength |
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Reflection | Resolution: 1.5→38 Å / Num. obs: 15111 / % possible obs: 99 % / Redundancy: 12 % / Rmerge(I) obs: 0.053 / Net I/σ(I): 77.6 | |||||||||
Reflection shell | Resolution: 1.5→1.62 Å / Redundancy: 7.7 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 3 / Num. unique obs: 2903 / % possible all: 87.5 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.501→37.958 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 15.23 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 47.703 Å2 / ksol: 0.398 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.501→37.958 Å
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Refine LS restraints |
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LS refinement shell |
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