+Open data
-Basic information
Entry | Database: PDB / ID: 4d5s | ||||||
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Title | Structure of A49 from Vaccinia Virus Western Reserve | ||||||
Components | A49R | ||||||
Keywords | VIRAL PROTEIN / POXVIRUS / B CELL LYMPHOMA 2 (BCL-2) FAMILY / INNATE IMMUNE MODULATOR / NUCLEAR FACTOR KAPPA B (NF-KB) | ||||||
Function / homology | Orthopoxvirus A49 / Orthopoxvirus A49R protein / protein sequestering activity / : / host cell cytoplasm / host cell nucleus / Protein A49R Function and homology information | ||||||
Biological species | VACCINIA VIRUS | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å | ||||||
Authors | Neidel, S. / Maluquer de Motes, C. / Mansur, D.S. / Strnadova, P. / Smith, G.L. / Graham, S.C. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2015 Title: Vaccinia Virus Protein A49 is an Unexpected Member of the B-Cell Lymphoma (Bcl)-2 Protein Family Authors: Neidel, S. / Maluquer De Motes, C. / Mansur, D.S. / Strnadova, P. / Smith, G.L. / Graham, S.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4d5s.cif.gz | 129.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4d5s.ent.gz | 103.1 KB | Display | PDB format |
PDBx/mmJSON format | 4d5s.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d5/4d5s ftp://data.pdbj.org/pub/pdb/validation_reports/d5/4d5s | HTTPS FTP |
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-Related structure data
Related structure data | 4d5rSC 4d5tC 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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Unit cell |
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-Components
#1: Protein | Mass: 19741.240 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) VACCINIA VIRUS / Strain: WESTERN RESERVE / Plasmid: POPINE / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA2 PLYSS / References: UniProt: P31037 Sequence details | CARRIES C-TERMINAL KH6 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: 2.22 Å3/Da / Density % sol: 44.5 % / Description: NONE |
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Crystal grow | Temperature: 294 K Details: FULL-LENGTH A49 (100 NL AT 9.5 MG/ML) WAS MIXED WITH 100 NL RESERVOIR SOLUTION AND EQUILIBRATED AT 21 C AGAINST 95 UL RESERVOIRS COMPRISING 25% (WT/VOL) PEG 3350, 0.2 M AMMONIUM SULFATE AND ...Details: FULL-LENGTH A49 (100 NL AT 9.5 MG/ML) WAS MIXED WITH 100 NL RESERVOIR SOLUTION AND EQUILIBRATED AT 21 C AGAINST 95 UL RESERVOIRS COMPRISING 25% (WT/VOL) PEG 3350, 0.2 M AMMONIUM SULFATE AND 0.1 M TRIS PH 9.5. CRYOPROTECTION WAS ACHIEVED BY QUICKLY SWEEPING THE CRYSTAL THROUGH RESERVOIR SUPPLEMENTED WITH 20% (VOL/VOL) GLYCEROL. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 12, 2008 / Details: TOROIDAL ZERODUR MIRROR |
Radiation | Monochromator: DIAMOND (ASYMMETRIC LAUE 001) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 3→50 Å / Num. obs: 7353 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 13.8 % / Biso Wilson estimate: 81.5 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 17.5 |
Reflection shell | Resolution: 3→3.05 Å / Redundancy: 14.4 % / Mean I/σ(I) obs: 2.2 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4D5R Resolution: 3→153.95 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.952 / SU B: 59.53 / SU ML: 0.421 / Cross valid method: THROUGHOUT / ESU R Free: 0.465 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 94.958 Å2
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Refinement step | Cycle: LAST / Resolution: 3→153.95 Å
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Refine LS restraints |
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