+Open data
-Basic information
Entry | Database: PDB / ID: 7ccm | ||||||
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Title | Crystal structure of selenomethionine-derived human BFK | ||||||
Components | Bcl-2-like protein 15 | ||||||
Keywords | APOPTOSIS / BCL-2 family kin | ||||||
Function / homology | Bcl-2-like protein 15 / Bcl-2-like superfamily / regulation of apoptotic process / apoptotic process / nucleus / cytosol / Bcl-2-like protein 15 Function and homology information | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.45 Å | ||||||
Authors | Oh, E.K. / Jang, D.M. / Han, B.W. | ||||||
Funding support | Korea, Republic Of, 1items
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Citation | Journal: To Be Published Title: Structural analyses on human BFK, a Novel BCL-2 Family Member. Authors: Jang, D.M. / Oh, E.K. / Han, B.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7ccm.cif.gz | 94.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7ccm.ent.gz | 73.3 KB | Display | PDB format |
PDBx/mmJSON format | 7ccm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7ccm_validation.pdf.gz | 437.1 KB | Display | wwPDB validaton report |
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Full document | 7ccm_full_validation.pdf.gz | 437.4 KB | Display | |
Data in XML | 7ccm_validation.xml.gz | 15.7 KB | Display | |
Data in CIF | 7ccm_validation.cif.gz | 21 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cc/7ccm ftp://data.pdbj.org/pub/pdb/validation_reports/cc/7ccm | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 20235.693 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: BCL2L15, C1orf178 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5TBC7 #2: Water | ChemComp-HOH / | Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 0.1 M Bis-Tris pH 5.5, 28% PEG 3350 |
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-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.97918 Å |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Nov 11, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 |
Reflection | Resolution: 2.45→50 Å / Num. obs: 15406 / % possible obs: 99.1 % / Redundancy: 3.1 % / CC1/2: 0.997 / Rmerge(I) obs: 0.071 / Net I/σ(I): 12.32 |
Reflection shell | Resolution: 2.45→2.49 Å / Redundancy: 2 % / Rmerge(I) obs: 0.784 / Mean I/σ(I) obs: 1.06 / Num. unique obs: 708 / CC1/2: 0.803 / % possible all: 90.9 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.45→38.05 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.904 / WRfactor Rfree: 0.236 / WRfactor Rwork: 0.198 / SU B: 12.053 / SU ML: 0.267 / Average fsc free: 0.8679 / Average fsc work: 0.8956 / Cross valid method: FREE R-VALUE / ESU R Free: 0.354 Details: Hydrogens have been added in their 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 BULK SOLVENT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 39.143 Å2
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Refinement step | Cycle: LAST / Resolution: 2.45→38.05 Å
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Refine LS restraints |
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LS refinement shell |
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