[English] 日本語
Yorodumi- PDB-8qdo: Crystal structure of the tegument protein UL82 (pp71) from Human ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8qdo | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of the tegument protein UL82 (pp71) from Human Cytomegalovirus | ||||||
Components | Protein pp71 | ||||||
Keywords | VIRAL PROTEIN / dUTPase fold / tegument protein / transactivator | ||||||
Function / homology | Herpesvirus UL82/UL83 / Betaherpesvirus UL82/83 protein N terminus / : / DNA-templated viral transcription / viral tegument / host cell endoplasmic reticulum / symbiont-mediated perturbation of host cell cycle G1/S transition checkpoint / host cell nucleus / Protein pp71 Function and homology information | ||||||
Biological species | Human betaherpesvirus 5 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.7 Å | ||||||
Authors | Bresch, I.P. / Eberhage, J. / Reubold, T.F. / Eschenburg, S. | ||||||
Funding support | Germany, 1items
| ||||||
Citation | Journal: Protein Sci. / Year: 2024 Title: Crystal structure of the tegument protein UL82 (pp71) from human cytomegalovirus. Authors: Eberhage, J. / Bresch, I.P. / Ramani, R. / Viohl, N. / Buchta, T. / Rehfeld, C.L. / Hinse, P. / Reubold, T.F. / Brinkmann, M.M. / Eschenburg, S. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 8qdo.cif.gz | 232 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb8qdo.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 8qdo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8qdo_validation.pdf.gz | 454.2 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 8qdo_full_validation.pdf.gz | 462.2 KB | Display | |
Data in XML | 8qdo_validation.xml.gz | 31.6 KB | Display | |
Data in CIF | 8qdo_validation.cif.gz | 42.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qd/8qdo ftp://data.pdbj.org/pub/pdb/validation_reports/qd/8qdo | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
---|
-Links
-Assembly
Deposited unit |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Unit cell |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Ens-ID: ens_1
NCS oper: (Code: givenMatrix: (-0.0203818160206, -0.989007489787, 0.146453974755), (-0.988595928809, -0.00192484142211, -0.150580159806), (0.149206806539, -0.147852900314, -0.977689546201)Vector: 59. ...NCS oper: (Code: given Matrix: (-0.0203818160206, -0.989007489787, 0.146453974755), Vector: |
-Components
#1: Protein | Mass: 62496.988 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human betaherpesvirus 5 / Strain: AD169 / Gene: UL82 / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P06726 #2: Chemical | ChemComp-PG4 / | #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.45 Å3/Da / Density % sol: 64.37 % |
---|---|
Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / Details: 0.1 M MES pH 6.5, 0.2 M MgCl2, 7.25% w/v PEG4000 |
-Data collection
Diffraction |
| ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source |
| ||||||||||||||||||
Detector |
| ||||||||||||||||||
Radiation |
| ||||||||||||||||||
Radiation wavelength |
| ||||||||||||||||||
Reflection | Resolution: 2.7→48.614 Å / Num. obs: 47593 / % possible obs: 100 % / Redundancy: 13.76 % / Biso Wilson estimate: 85.38 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.075 / Rsym value: 0.072 / Net I/σ(I): 22.55 | ||||||||||||||||||
Reflection shell | Resolution: 2.7→2.8 Å / Redundancy: 14.4 % / Mean I/σ(I) obs: 2.11 / Num. unique obs: 4846 / CC1/2: 0.793 / Rrim(I) all: 1.209 / Rsym value: 1.167 / % possible all: 100 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: SAD / Resolution: 2.7→48.61 Å / SU ML: 0.4785 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 24.8578 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 81.72 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.7→48.61 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints NCS | Type: Torsion NCS / Rms dev position: 0.861718070637 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|