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Yorodumi- PDB-4qkb: Crystal structure of seleno-methionine labelled human ALKBH7 in c... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4qkb | ||||||
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Title | Crystal structure of seleno-methionine labelled human ALKBH7 in complex with alpha-ketoglutarate and Mn(II) | ||||||
Components | Alpha-ketoglutarate-dependent dioxygenase alkB homolog 7, mitochondrial | ||||||
Keywords | OXIDOREDUCTASE / alkbh7 / DIOXYGENASE / METAL-BINDING / programmed necrosis / fat metabolism | ||||||
Function / homology | Function and homology information regulation of lipid storage / regulation of mitochondrial membrane permeability involved in programmed necrotic cell death / Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With 2-oxoglutarate as one donor, and incorporation of one atom of oxygen into each donor / dioxygenase activity / fatty acid metabolic process / mitochondrial matrix / DNA damage response / mitochondrion / metal ion binding Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.6 Å | ||||||
Authors | Wang, G. / He, Q. / Chen, Z. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2014 Title: The atomic resolution structure of human AlkB homolog 7 (ALKBH7), a key protein for programmed necrosis and fat metabolism Authors: Wang, G. / He, Q. / Feng, C. / Liu, Y. / Deng, Z. / Qi, X. / Wu, W. / Mei, P. / Chen, Z. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4qkb.cif.gz | 120.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4qkb.ent.gz | 99.3 KB | Display | PDB format |
PDBx/mmJSON format | 4qkb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4qkb_validation.pdf.gz | 466 KB | Display | wwPDB validaton report |
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Full document | 4qkb_full_validation.pdf.gz | 470.1 KB | Display | |
Data in XML | 4qkb_validation.xml.gz | 22.6 KB | Display | |
Data in CIF | 4qkb_validation.cif.gz | 30.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qk/4qkb ftp://data.pdbj.org/pub/pdb/validation_reports/qk/4qkb | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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2 |
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3 |
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4 |
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Unit cell |
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-Components
#1: Protein | Mass: 22804.123 Da / Num. of mol.: 3 / Fragment: UNP RESIDUES 17-215 / Mutation: Q90R, R86M and L89M Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ABH7, ALKBH7, SPATA11, UNQ6002/PRO34564 / Production host: Escherichia coli (E. coli) References: UniProt: Q9BT30, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With 2-oxoglutarate as one donor, and incorporation of one atom of oxygen into each donor #2: Chemical | ChemComp-MN / #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 3 |
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-Sample preparation
Crystal | Density Matthews: 2.33 Å3/Da / Density % sol: 47.29 % |
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Crystal grow | Temperature: 277 K / Method: evaporation / pH: 6 / Details: PEG pH6, EVAPORATION, temperature 277K |
-Data collection
Diffraction | Mean temperature: 130 K | |||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 0.97929, 0.97943 | |||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: May 11, 2013 | |||||||||||||||||||||||||||||||||||
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||
Radiation wavelength |
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Reflection twin |
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Reflection | Resolution: 2.6→50.01 Å / Num. all: 19493 / Num. obs: 17632 / % possible obs: 90.5 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 | |||||||||||||||||||||||||||||||||||
Reflection shell | Resolution: 2.6→2.64 Å / % possible all: 51 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.6→50 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.919 / SU B: 13.736 / SU ML: 0.282 / Cross valid method: THROUGHOUT / σ(F): 3 / ESU R Free: 0.055 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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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: 27.651 Å2
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Refinement step | Cycle: LAST / Resolution: 2.6→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.596→2.663 Å / Total num. of bins used: 20
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