+Open data
-Basic information
Entry | Database: PDB / ID: 5vwv | ||||||||||||
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Title | Bak core latch dimer in complex with Bim-BH3 - Cubic | ||||||||||||
Components |
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Keywords | APOPTOSIS / Bcl-2 Family / Activator | ||||||||||||
Function / homology | Function and homology information dynorphin receptor activity / neuropeptide binding / neuropeptide signaling pathway / sensory perception of pain / toxin activity / neuron projection / extracellular region / membrane Similarity search - Function | ||||||||||||
Biological species | Homo sapiens (human) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.897 Å | ||||||||||||
Authors | Brouwer, J.M. / Colman, P.M. / Czabotar, P.E. | ||||||||||||
Funding support | Australia, 3items
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Citation | Journal: Mol. Cell / Year: 2017 Title: Conversion of Bim-BH3 from Activator to Inhibitor of Bak through Structure-Based Design. Authors: Brouwer, J.M. / Lan, P. / Cowan, A.D. / Bernardini, J.P. / Birkinshaw, R.W. / van Delft, M.F. / Sleebs, B.E. / Robin, A.Y. / Wardak, A. / Tan, I.K. / Reljic, B. / Lee, E.F. / Fairlie, W.D. / ...Authors: Brouwer, J.M. / Lan, P. / Cowan, A.D. / Bernardini, J.P. / Birkinshaw, R.W. / van Delft, M.F. / Sleebs, B.E. / Robin, A.Y. / Wardak, A. / Tan, I.K. / Reljic, B. / Lee, E.F. / Fairlie, W.D. / Call, M.J. / Smith, B.J. / Dewson, G. / Lessene, G. / Colman, P.M. / Czabotar, P.E. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5vwv.cif.gz | 101.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5vwv.ent.gz | 77.5 KB | Display | PDB format |
PDBx/mmJSON format | 5vwv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5vwv_validation.pdf.gz | 459.1 KB | Display | wwPDB validaton report |
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Full document | 5vwv_full_validation.pdf.gz | 459.6 KB | Display | |
Data in XML | 5vwv_validation.xml.gz | 11.9 KB | Display | |
Data in CIF | 5vwv_validation.cif.gz | 16.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vw/5vwv ftp://data.pdbj.org/pub/pdb/validation_reports/vw/5vwv | HTTPS FTP |
-Related structure data
Related structure data | 5vwwC 5vwxC 5vwyC 5vwzC 5vx0C 5vx1C 5vx2C 5vx3C C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
-Protein / Protein/peptide , 2 types, 2 molecules AB
#1: Protein | Mass: 19037.320 Da / Num. of mol.: 1 / Fragment: UNP residues 23-186 / Mutation: C166S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: BAK1, BAK, BCL2L7, CDN1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q16611 |
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#2: Protein/peptide | Mass: 3026.411 Da / Num. of mol.: 1 / Fragment: UNP residues 141-165 / Mutation: W147R, Y163T / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: O43521 |
-Non-polymers , 5 types, 195 molecules
#3: Chemical | ChemComp-TFA / | ||||||
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#4: Chemical | ChemComp-EDO / #5: Chemical | ChemComp-CL / | #6: Chemical | ChemComp-GOL / | #7: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 5.12 Å3/Da / Density % sol: 75.96 % |
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Crystal grow | Temperature: 281 K / Method: vapor diffusion, sitting drop Details: 18 % glycerol, 21.6 % PEG (poly-ethylene glycol) 1500 and 0.5 % ethyl acetate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 12, 2014 |
Radiation | Monochromator: ADSC QUANTUM 315r / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 |
Reflection | Resolution: 1.897→42.032 Å / Num. obs: 37157 / % possible obs: 100 % / Redundancy: 47.8 % / Rmerge(I) obs: 0.2162 / Net I/σ(I): 24.26 |
Reflection shell | Resolution: 1.898→1.966 Å / Redundancy: 47 % / Mean I/σ(I) obs: 1.48 / Num. unique obs: 3647 / CC1/2: 0.497 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.897→42.032 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 16.3
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.897→42.032 Å
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Refine LS restraints |
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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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