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Yorodumi- PDB-5i8t: Structure of Mouse Acireductone dioxygenase with Ni2+ ion and D-l... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5i8t | |||||||||
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Title | Structure of Mouse Acireductone dioxygenase with Ni2+ ion and D-lactic acid in the active site | |||||||||
Components | 1,2-dihydroxy-3-keto-5-methylthiopentene dioxygenase | |||||||||
Keywords | OXIDOREDUCTASE / Substrate analog / D-lactic acid | |||||||||
Function / homology | Function and homology information Methionine salvage pathway / acireductone dioxygenase (Ni2+-requiring) / acireductone dioxygenase [iron(II)-requiring] / acireductone dioxygenase (Ni2+-requiring) activity / acireductone dioxygenase [iron(II)-requiring] activity / methionine metabolic process / L-methionine salvage from methylthioadenosine / nickel cation binding / oxidoreductase activity / iron ion binding ...Methionine salvage pathway / acireductone dioxygenase (Ni2+-requiring) / acireductone dioxygenase [iron(II)-requiring] / acireductone dioxygenase (Ni2+-requiring) activity / acireductone dioxygenase [iron(II)-requiring] activity / methionine metabolic process / L-methionine salvage from methylthioadenosine / nickel cation binding / oxidoreductase activity / iron ion binding / nucleus / plasma membrane / cytoplasm Similarity search - Function | |||||||||
Biological species | Mus musculus (house mouse) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.751 Å | |||||||||
Authors | Deshpande, A.R. / Wagenpfeil, K. / Pochapsky, T.C. / Petsko, G.A. / Ringe, D. | |||||||||
Funding support | United States, 1items
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Citation | Journal: Biochemistry / Year: 2016 Title: Metal-Dependent Function of a Mammalian Acireductone Dioxygenase. Authors: Deshpande, A.R. / Wagenpfeil, K. / Pochapsky, T.C. / Petsko, G.A. / Ringe, D. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5i8t.cif.gz | 64 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5i8t.ent.gz | 44.2 KB | Display | PDB format |
PDBx/mmJSON format | 5i8t.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5i8t_validation.pdf.gz | 451.7 KB | Display | wwPDB validaton report |
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Full document | 5i8t_full_validation.pdf.gz | 453.5 KB | Display | |
Data in XML | 5i8t_validation.xml.gz | 13.2 KB | Display | |
Data in CIF | 5i8t_validation.cif.gz | 19.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i8/5i8t ftp://data.pdbj.org/pub/pdb/validation_reports/i8/5i8t | HTTPS FTP |
-Related structure data
Related structure data | 5i8sC 5i8yC 5i91C 5i93C 1vr3S C: citing same article (ref.) 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
#1: Protein | Mass: 21554.574 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Adi1, Mtcbp1 / Plasmid: pMH4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIPL strain References: UniProt: Q99JT9, acireductone dioxygenase [iron(II)-requiring] |
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#2: Chemical | ChemComp-NI / |
#3: Chemical | ChemComp-LAC / |
#4: Chemical | ChemComp-IPA / |
#5: 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: 4.17 Å3/Da / Density % sol: 70.48 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: 5.0% Glycerol, 19.0% iso-Propanol, 19.0% PEG-4000, 0.1M Citrate pH 5.6 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9793 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 10, 2015 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.75→50 Å / Num. obs: 37413 / % possible obs: 99.9 % / Redundancy: 11.8 % / Rmerge(I) obs: 0.076 / Rpim(I) all: 0.023 / Rrim(I) all: 0.08 / Χ2: 0.835 / Net I/av σ(I): 32.933 / Net I/σ(I): 6.2 / Num. measured all: 439867 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1VR3 Resolution: 1.751→27.151 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.54
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 74.67 Å2 / Biso mean: 28.1537 Å2 / Biso min: 13.31 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.751→27.151 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14 / % reflection obs: 100 %
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