+Open data
-Basic information
Entry | Database: PDB / ID: 2vvx | ||||||
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Title | Structure of Vaccinia virus protein A52 | ||||||
Components | PROTEIN A52 | ||||||
Keywords | VIRAL PROTEIN / IRAK2 / TRAF6 / BCL-2 FAMILY / VACCINIA VIRUS / IMMUNOMODULATOR / NF-KB ACTIVATION / HOST-VIRUS INTERACTION | ||||||
Function / homology | Function and homology information : / symbiont-mediated suppression of host TRAF-mediated signal transduction / protein sequestering activity / : / host cell cytoplasm Similarity search - Function | ||||||
Biological species | VACCINIA VIRUS | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.746 Å | ||||||
Authors | Graham, S.C. / Bahar, M.W. / Cooray, S. / Chen, R.A.-J. / Whalen, D.M. / Abrescia, N.G.A. / Alderton, D. / Owens, R.J. / Stuart, D.I. / Smith, G.L. / Grimes, J.M. | ||||||
Citation | Journal: Plos Pathog. / Year: 2008 Title: Vaccinia Virus Proteins A52 and B14 Share a Bcl-2-Like Fold But Have Evolved to Inhibit NF-kappaB Rather Than Apoptosis Authors: Graham, S.C. / Bahar, M.W. / Cooray, S. / Chen, R.A.-J. / Whalen, D.M. / Abrescia, N.G.A. / Alderton, D. / Owens, R.J. / Stuart, D.I. / Smith, G.L. / Grimes, J.M. | ||||||
History |
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Remark 650 | HELIX DETERMINATION METHOD: AUTHOR PROVIDED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2vvx.cif.gz | 138.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2vvx.ent.gz | 110.5 KB | Display | PDB format |
PDBx/mmJSON format | 2vvx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vv/2vvx ftp://data.pdbj.org/pub/pdb/validation_reports/vv/2vvx | HTTPS FTP |
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-Related structure data
Related structure data | 2vvwSC 2vvyC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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3 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
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-Components
#1: Protein | Mass: 19589.703 Da / Num. of mol.: 2 / Fragment: RESIDUES 37-190 Source method: isolated from a genetically manipulated source Source: (gene. exp.) VACCINIA VIRUS / Strain: WESTERN RESERVE / Plasmid: POPINF / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): ROSETTA(DE3) PLYSS / References: UniProt: Q01220 Sequence details | RESIDUES 1-36 ARE REMOVED, AN N-TERMINAL START CODON IS ADDED AND A C-TERMINAL LYS-HIS6 ...RESIDUES 1-36 ARE REMOVED, AN N-TERMINAL START CODON IS ADDED AND A C-TERMINAL LYS-HIS6 PURIFICATI | |
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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: 4.88 Å3/Da / Density % sol: 74.83 % Description: MODEL WAS STRIPPED OF SOLVENT AND ALTERNATE CONFORMATIONS PRIOR TO MOLECULAR REPLACEMENT. |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop Details: HANGING DROPS CONTAINING 1 UL PROTEIN (5.4 MG/ML IN 20 MM TRIS, 200 MM NACL, PH 7.5) AND 1 UL RESERVOIR SOLUTION (0.2 M SODIUM PHOSPHATE, 22% (W/V) PEG 3350) WERE EQUILIBRATED AGAINST 500 UL ...Details: HANGING DROPS CONTAINING 1 UL PROTEIN (5.4 MG/ML IN 20 MM TRIS, 200 MM NACL, PH 7.5) AND 1 UL RESERVOIR SOLUTION (0.2 M SODIUM PHOSPHATE, 22% (W/V) PEG 3350) WERE EQUILIBRATED AGAINST 500 UL RESERVOIRS AT 21 C. CRYSTALS WERE CRYOPROTECTED IN RESERVOIR SOLUTION SUPPLEMENTED WITH 20% (V/V) GLYCEROL. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 1.06 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Sep 11, 2007 / Details: MIRRORS |
Radiation | Monochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.06 Å / Relative weight: 1 |
Reflection | Resolution: 2.75→50 Å / Num. obs: 19184 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 5.7 % / Biso Wilson estimate: 56.92 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 13.8 |
Reflection shell | Resolution: 2.75→2.8 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.82 / Mean I/σ(I) obs: 2.1 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2VVW, CHAIN A Resolution: 2.746→40.981 Å / SU ML: 0.23 / Phase error: 21.3 / Stereochemistry target values: ML / Details: B VALUES INCLUDE TLS CONTRIBUTIONS.
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 56.898 Å2 / ksol: 0.335 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 81.77 Å2
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Refinement step | Cycle: LAST / Resolution: 2.746→40.981 Å
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Refine LS restraints |
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Refine LS restraints NCS |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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