+Open data
-Basic information
Entry | Database: PDB / ID: 4bbb | ||||||
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Title | THE STRUCTURE OF VACCINIA VIRUS N1 Q61Y MUTANT | ||||||
Components | N1L | ||||||
Keywords | VIRAL PROTEIN / BCL-LIKE PROTEIN / APOPTOSIS / VIRULENCE FACTOR | ||||||
Function / homology | Function and homology information symbiont-mediated perturbation of host apoptosis / symbiont-mediated suppression of host NF-kappaB cascade / virus-mediated perturbation of host defense response Similarity search - Function | ||||||
Biological species | VACCINIA VIRUS | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.09 Å | ||||||
Authors | Maluquer de Motes, C. / Cooray, S. / McGourty, K. / Ren, H. / Bahar, M.W. / Stuart, D.I. / Grimes, J.M. / Graham, S.C. / Smith, G.L. | ||||||
Citation | Journal: Plos Pathog. / Year: 2011 Title: Inhibition of Apoptosis and NF-kappaB Activation by Vaccinia Protein N1 Occur Via Distinct Binding Surfaces and Make Different Contributions to Virulence. Authors: Maluquer De Motes, C. / Cooray, S. / Ren, H. / Almeida, G.M.F. / Mcgourty, K. / Bahar, M.W. / Stuart, D.I. / Grimes, J.M. / Graham, S.C. / Smith, G.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4bbb.cif.gz | 296.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4bbb.ent.gz | 247.4 KB | Display | PDB format |
PDBx/mmJSON format | 4bbb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4bbb_validation.pdf.gz | 457 KB | Display | wwPDB validaton report |
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Full document | 4bbb_full_validation.pdf.gz | 459.3 KB | Display | |
Data in XML | 4bbb_validation.xml.gz | 21.2 KB | Display | |
Data in CIF | 4bbb_validation.cif.gz | 30.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bb/4bbb ftp://data.pdbj.org/pub/pdb/validation_reports/bb/4bbb | HTTPS FTP |
-Related structure data
Related structure data | 4bbcC 4bbdC 2i39S 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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-Components
#1: Protein | Mass: 15068.172 Da / Num. of mol.: 6 / Mutation: YES Source method: isolated from a genetically manipulated source Details: C40S MUTATION WAS INTRODUCED TO AVOID INTERMOLECULAR DISULPHIDE BOND DRIVEN AGGREGATION. Source: (gene. exp.) VACCINIA VIRUS / Strain: WESTERN RESERVE / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): B834 / References: UniProt: Q49PX0, UniProt: P21054*PLUS Sequence details | Q61Y IS FUNCTIONAL MUTATION. C40S MUTATION WAS INTRODUCED TO AVOID INTERMOLECULAR DISULPHIDE BOND ...Q61Y IS FUNCTIONAL | |
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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: 2.78 Å3/Da / Density % sol: 55.82 % Description: SOLVED BY ISOMORPHOUS DIFFERENCE FOURIER SYNTHESIS. |
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Crystal grow | pH: 7 / Details: pH 7 |
-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 CCD / Detector: CCD / Date: Dec 12, 2008 / Details: TOROIDAL ZERODUR MIRROR |
Radiation | Monochromator: 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: 3.1→42.2 Å / Num. obs: 18168 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Biso Wilson estimate: 105.85 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 13.3 |
Reflection shell | Resolution: 3.09→3.28 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.99 / Mean I/σ(I) obs: 1.6 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ID 2I39 Resolution: 3.09→42.15 Å / Cor.coef. Fo:Fc: 0.9558 / Cor.coef. Fo:Fc free: 0.9365 / Cross valid method: THROUGHOUT / σ(F): 0 Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. ALL ATOMS HAVE CCP4 ATOM TYPE FROM LIBRARY
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Displacement parameters | Biso mean: 106.37 Å2
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Refine analyze | Luzzati coordinate error obs: 0.773 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.09→42.15 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.09→3.28 Å / Total num. of bins used: 9
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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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