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Yorodumi- PDB-4hlx: The crystal structure of the DNA binding domain of vIRF-1 from th... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4hlx | ||||||
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Title | The crystal structure of the DNA binding domain of vIRF-1 from the oncogenic KSHV | ||||||
Components | K9 | ||||||
Keywords | DNA BINDING PROTEIN / helix-turn-helix | ||||||
Function / homology | Function and homology information transcription cis-regulatory region binding / DNA-binding transcription factor activity Similarity search - Function | ||||||
Biological species | Human herpesvirus 8 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.379 Å | ||||||
Authors | Hew, K. / Venkatachalam, R. | ||||||
Citation | Journal: Nucleic Acids Res. / Year: 2013 Title: The crystal structure of the DNA-binding domain of vIRF-1 from the oncogenic KSHV reveals a conserved fold for DNA binding and reinforces its role as a transcription factor. Authors: Hew, K. / Dahlroth, S.L. / Venkatachalam, R. / Nasertorabi, F. / Lim, B.T. / Cornvik, T. / Nordlund, P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4hlx.cif.gz | 89.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4hlx.ent.gz | 72.9 KB | Display | PDB format |
PDBx/mmJSON format | 4hlx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4hlx_validation.pdf.gz | 456.5 KB | Display | wwPDB validaton report |
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Full document | 4hlx_full_validation.pdf.gz | 459.3 KB | Display | |
Data in XML | 4hlx_validation.xml.gz | 15.8 KB | Display | |
Data in CIF | 4hlx_validation.cif.gz | 22.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hl/4hlx ftp://data.pdbj.org/pub/pdb/validation_reports/hl/4hlx | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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4 |
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Unit cell |
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-Components
#1: Protein | Mass: 15309.481 Da / Num. of mol.: 4 / Fragment: DNA binding domain, UNP RESIDUES 88-196 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human herpesvirus 8 / Gene: ORF K9, vIRF, vIRF-1 / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-DE3-Rosetta / References: UniProt: Q77Q82 #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.98 Å3/Da / Density % sol: 37.75 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 0.1 M HEPES pH 7, 27% Jeffamine-ED 2001, 10 mM ATP, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 0.96722 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 28, 2011 |
Radiation | Monochromator: Rh Coated Mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.96722 Å / Relative weight: 1 |
Reflection | Resolution: 2.379→23.292 Å / Num. all: 18285 / Num. obs: 18285 / % possible obs: 92.5 % / Redundancy: 6.6 % |
Reflection shell | Highest resolution: 2.38 Å / Redundancy: 6.6 % / Num. unique all: 18285 / % possible all: 92.58 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.379→23.292 Å / SU ML: 0.36 / σ(F): 1.42 / Phase error: 32.12 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.379→23.292 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6
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