+Open data
-Basic information
Entry | Database: PDB / ID: 5b1q | ||||||
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Title | Human herpesvirus 6B tegument protein U14 | ||||||
Components | U14 protein | ||||||
Keywords | VIRAL PROTEIN / Herpesvirus / Tegument / Homodimer | ||||||
Function / homology | Herpesvirus phosphoprotein 85 (HHV6-7 U14/HCMV UL25) / Herpesvirus phosphoprotein 85 (HHV6-7 U14/HCMV UL25) / U14 protein Function and homology information | ||||||
Biological species | Human herpesvirus 6B | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.85 Å | ||||||
Authors | Wang, B. / Nishimura, M. / Tang, H. / Kawabata, A. / Mahmoud, N.F. / Khanlari, Z. / Hamada, D. / Tsuruta, H. / Mori, Y. | ||||||
Citation | Journal: Plos Pathog. / Year: 2016 Title: Crystal Structure of Human Herpesvirus 6B Tegument Protein U14. Authors: Wang, B. / Nishimura, M. / Tang, H. / Kawabata, A. / Mahmoud, N.F. / Khanlari, Z. / Hamada, D. / Tsuruta, H. / Mori, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5b1q.cif.gz | 217.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5b1q.ent.gz | 171.2 KB | Display | PDB format |
PDBx/mmJSON format | 5b1q.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5b1q_validation.pdf.gz | 450.2 KB | Display | wwPDB validaton report |
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Full document | 5b1q_full_validation.pdf.gz | 455.3 KB | Display | |
Data in XML | 5b1q_validation.xml.gz | 44.1 KB | Display | |
Data in CIF | 5b1q_validation.cif.gz | 68.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b1/5b1q ftp://data.pdbj.org/pub/pdb/validation_reports/b1/5b1q | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 52669.332 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 2-458 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human herpesvirus 6B (strain HST) / Strain: HST / Gene: U14 / Plasmid: pMAL-C2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q9WT50 #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.58 Å3/Da / Density % sol: 52.41 % |
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Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 7.2 Details: 0.2M Potassium sodium tartrate tetrahydrate, 16-18% w/v Polyethylene glycol 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 1 Å |
Detector | Type: RAYONIX MX-225 / Detector: CCD / Date: Nov 19, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→46.68 Å / Num. obs: 93926 / % possible obs: 99.75 % / Redundancy: 7.2 % / Rmerge(I) obs: 0.08735 / Net I/σ(I): 18.04 |
Reflection shell | Resolution: 1.85→1.92 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.575 / Mean I/σ(I) obs: 3.39 / % possible all: 99.13 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.85→46.68 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.21 / Phase error: 21.5 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.85→46.68 Å
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Refine LS restraints |
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LS refinement shell |
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