+Open data
-Basic information
Entry | Database: PDB / ID: 3r8k | ||||||
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Title | Crystal structure of human SOUL protein (hexagonal form) | ||||||
Components | Heme-binding protein 2 | ||||||
Keywords | APOPTOSIS / HEBP family / SOUL protein | ||||||
Function / homology | Function and homology information azurophil granule lumen / heme binding / Neutrophil degranulation / mitochondrion / extracellular exosome / extracellular region / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 Å | ||||||
Authors | Ambrosi, E.K. / Capaldi, S. / Bovi, M. / Saccomani, G. / Perduca, M. / Monaco, H.L. | ||||||
Citation | Journal: Biochem.J. / Year: 2011 Title: Structural changes in the BH3 domain of SOUL protein upon interaction with the anti-apoptotic protein Bcl-xL. Authors: Ambrosi, E. / Capaldi, S. / Bovi, M. / Saccomani, G. / Perduca, M. / Monaco, H.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3r8k.cif.gz | 147.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3r8k.ent.gz | 118.5 KB | Display | PDB format |
PDBx/mmJSON format | 3r8k.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3r8k_validation.pdf.gz | 454.9 KB | Display | wwPDB validaton report |
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Full document | 3r8k_full_validation.pdf.gz | 473.9 KB | Display | |
Data in XML | 3r8k_validation.xml.gz | 27.7 KB | Display | |
Data in CIF | 3r8k_validation.cif.gz | 36.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r8/3r8k ftp://data.pdbj.org/pub/pdb/validation_reports/r8/3r8k | HTTPS FTP |
-Related structure data
Related structure data | 3r85C 3r8jSC 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: 23663.248 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: C6orf34, HEBP2, SOUL / Plasmid: pQE50 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 C41 / References: UniProt: Q9Y5Z4 |
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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: 3.82 Å3/Da / Density % sol: 67.83 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 2.0M ammonium sulphate, 0.1M Tris-HCl, 0.2M 1-butyl-3-methylimidazolium chloride, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9795 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 14, 2008 |
Radiation | Monochromator: Channel cut ESRF monochromator, crystal type: Si(111) Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.85→55.4 Å / Num. all: 35307 / Num. obs: 35245 / % possible obs: 99.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 20.5 % / Rmerge(I) obs: 0.085 / Net I/σ(I): 25.7 |
Reflection shell | Resolution: 2.85→2.95 Å / Redundancy: 20.4 % / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 8.3 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3R8J Resolution: 2.85→55.4 Å / SU ML: 0.49 / σ(F): 1.76 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 41.415 Å2 / ksol: 0.322 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.85→55.4 Å
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Refine LS restraints |
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LS refinement shell |
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