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Yorodumi- PDB-2jbx: Crystal Structure of the myxoma virus anti-apoptotic protein M11L -
+Open data
-Basic information
Entry | Database: PDB / ID: 2jbx | ||||||
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Title | Crystal Structure of the myxoma virus anti-apoptotic protein M11L | ||||||
Components | M11L PROTEIN | ||||||
Keywords | APOPTOSIS / BCL-2 FAMILY / MYXOMA VIRUS | ||||||
Function / homology | Function and homology information | ||||||
Biological species | MYXOMA VIRUS | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.73 Å | ||||||
Authors | Kvansakul, M. / Van Delft, M.F. / Lee, E.F. / Gulbis, J.M. / Fairlie, W.D. / Huang, D.C.S. / Colman, P.M. | ||||||
Citation | Journal: Mol.Cell / Year: 2007 Title: A Structural Viral Mimic of Prosurvival Bcl-2: A Pivotal Role for Sequestering Proapoptotic Bax and Bak. Authors: Kvansakul, M. / Van Delft, M.F. / Lee, E.F. / Gulbis, J.M. / Fairlie, W.D. / Huang, D.C.S. / Colman, P.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2jbx.cif.gz | 65.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2jbx.ent.gz | 49.8 KB | Display | PDB format |
PDBx/mmJSON format | 2jbx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2jbx_validation.pdf.gz | 433.5 KB | Display | wwPDB validaton report |
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Full document | 2jbx_full_validation.pdf.gz | 446.9 KB | Display | |
Data in XML | 2jbx_validation.xml.gz | 14 KB | Display | |
Data in CIF | 2jbx_validation.cif.gz | 18.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jb/2jbx ftp://data.pdbj.org/pub/pdb/validation_reports/jb/2jbx | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 16881.328 Da / Num. of mol.: 2 / Fragment: RESIDUES 1-132 Source method: isolated from a genetically manipulated source Source: (gene. exp.) MYXOMA VIRUS / Strain: LAUSANNE / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): PLYZ / References: UniProt: Q85295 #2: Water | ChemComp-HOH / | |
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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: 2.19 Å3/Da / Density % sol: 43.82 % / Description: PDB ENTRY FOR M11L BAK COMPLEX TO BE SUBMITTED |
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Crystal grow | pH: 7.2 Details: 1.8 M AMMONIUM SULFATE, 10 MM KSCN, 100 MM HEPES PH 7.2 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 |
Detector | Type: RIGAKU IMAGE PLATE / Detector: IMAGE PLATE / Date: Dec 7, 2005 / Details: AXCO CAPILLARY OPTICS |
Radiation | Monochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.73→20 Å / Num. obs: 7483 / % possible obs: 97.3 % / Observed criterion σ(I): 3 / Redundancy: 2.7 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 9 |
Reflection shell | Resolution: 2.73→2.83 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 3 / % possible all: 91.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: M11L BAK COMPLEX Resolution: 2.73→20 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.839 / SU B: 18.914 / SU ML: 0.387 / Cross valid method: THROUGHOUT / ESU R Free: 0.445 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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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: 42.84 Å2
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Refinement step | Cycle: LAST / Resolution: 2.73→20 Å
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