+Open data
-Basic information
Entry | Database: PDB / ID: 5zb3 | |||||||||
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Title | Dimeric crystal structure of ORF57 from KSHV | |||||||||
Components | ORF57 | |||||||||
Keywords | TRANSCRIPTION / KSHV ORF57 | |||||||||
Function / homology | Herpesvirus ICP27-like / Herpesvirus transcriptional regulator family / host cell cytoplasm / host cell nucleus / regulation of DNA-templated transcription / RNA binding / metal ion binding / ORF57 / mRNA export factor ICP27 homolog Function and homology information | |||||||||
Biological species | Human herpesvirus 8 | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.506 Å | |||||||||
Authors | Gao, Z.Q. / Yuan, F. / Dong, Y.H. / Lan, K. | |||||||||
Funding support | China, 2items
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Citation | Journal: PLoS Pathog. / Year: 2018 Title: The crystal structure of KSHV ORF57 reveals dimeric active sites important for protein stability and function. Authors: Yuan, F. / Gao, Z.Q. / Majerciak, V. / Bai, L. / Hu, M.L. / Lin, X.X. / Zheng, Z.M. / Dong, Y.H. / Lan, K. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5zb3.cif.gz | 236.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5zb3.ent.gz | 193.3 KB | Display | PDB format |
PDBx/mmJSON format | 5zb3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5zb3_validation.pdf.gz | 817.2 KB | Display | wwPDB validaton report |
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Full document | 5zb3_full_validation.pdf.gz | 828 KB | Display | |
Data in XML | 5zb3_validation.xml.gz | 22.3 KB | Display | |
Data in CIF | 5zb3_validation.cif.gz | 29.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zb/5zb3 ftp://data.pdbj.org/pub/pdb/validation_reports/zb/5zb3 | HTTPS FTP |
-Related 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: 32237.393 Da / Num. of mol.: 2 / Fragment: C-terminal domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human herpesvirus 8 / Gene: ORF57 / Plasmid: pET-28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0A0N9SHG8, UniProt: Q2HR75*PLUS #2: Chemical | |
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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: 7.15 Å3/Da / Density % sol: 82.8 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 0.01M Magnesium chloride, 0.05M Hepes sodium pH 7.0, 4M Lithium chloride |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9792 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 5, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 3.5→50 Å / Num. obs: 24306 / % possible obs: 99.8 % / Redundancy: 10.3 % / CC1/2: 0.955 / Rmerge(I) obs: 0.141 / Rpim(I) all: 0.046 / Rrim(I) all: 0.149 / Net I/σ(I): 26.4 |
Reflection shell | Resolution: 3.5→3.56 Å / Redundancy: 10.5 % / Rmerge(I) obs: 0.805 / Mean I/σ(I) obs: 3.7 / Num. unique obs: 1185 / CC1/2: 0.948 / Rpim(I) all: 0.259 / Rrim(I) all: 0.846 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Resolution: 3.506→33.149 Å / SU ML: 0.43 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 34.42
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.506→33.149 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 62.7194 Å / Origin y: -58.2424 Å / Origin z: -14.0732 Å
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Refinement TLS group | Selection details: all |