+Open data
-Basic information
Entry | Database: PDB / ID: 6v4m | ||||||
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Title | Trichuris suis BCL-2 | ||||||
Components | BCL-2 | ||||||
Keywords | APOPTOSIS / BCL-2 / helical bundle | ||||||
Function / homology | Function and homology information regulation of apoptotic process / membrane => GO:0016020 / apoptotic process Similarity search - Function | ||||||
Biological species | Trichuris suis (pig whipworm) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.599 Å | ||||||
Authors | Fairlie, W.D. / Lee, E.F. / Smith, B.J. | ||||||
Citation | Journal: Commun Biol / Year: 2020 Title: Diversity in the intrinsic apoptosis pathway of nematodes. Authors: Young, N.D. / Harris, T.J. / Evangelista, M. / Tran, S. / Wouters, M.A. / Soares da Costa, T.P. / Kershaw, N.J. / Gasser, R.B. / Smith, B.J. / Lee, E.F. / Fairlie, W.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6v4m.cif.gz | 85.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6v4m.ent.gz | 63 KB | Display | PDB format |
PDBx/mmJSON format | 6v4m.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6v4m_validation.pdf.gz | 261.2 KB | Display | wwPDB validaton report |
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Full document | 6v4m_full_validation.pdf.gz | 261.2 KB | Display | |
Data in XML | 6v4m_validation.xml.gz | 1.1 KB | Display | |
Data in CIF | 6v4m_validation.cif.gz | 3.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v4/6v4m ftp://data.pdbj.org/pub/pdb/validation_reports/v4/6v4m | HTTPS FTP |
-Related structure data
Related structure data | 3fdlS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 19572.486 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Trichuris suis (pig whipworm) / Gene: M513_07322, M514_07322 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A085NFU1 | ||||||
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#2: Chemical | #3: Chemical | ChemComp-SO4 / | #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.17 Å3/Da / Density % sol: 43.28 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.1M Tris-chloride pH8.5, 0.2M Lithium sulphate, 2M sodium chloride |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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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: Nov 6, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 |
Reflection | Resolution: 1.599→39.199 Å / Num. obs: 23576 / % possible obs: 99.9 % / Redundancy: 14.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.078 / Net I/σ(I): 25.15 |
Reflection shell | Resolution: 1.6→1.7 Å / Redundancy: 14.2 % / Rmerge(I) obs: 0.76 / Mean I/σ(I) obs: 3.94 / Num. unique obs: 3723 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3FDL Chain A Resolution: 1.599→39.199 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 17.46
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 99.44 Å2 / Biso mean: 21.1672 Å2 / Biso min: 8.87 Å2 | |||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.599→39.199 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %
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Refinement TLS params. | Method: refined / Origin x: 36.4645 Å / Origin y: -5.4155 Å / Origin z: 38.9164 Å
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Refinement TLS group |
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