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Yorodumi- PDB-1mp0: Binary Complex of Human Glutathione-Dependent Formaldehyde Dehydr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1mp0 | ||||||
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Title | Binary Complex of Human Glutathione-Dependent Formaldehyde Dehydrogenase with NAD(H) | ||||||
Components | alcohol dehydrogenase class III chi chain | ||||||
Keywords | OXIDOREDUCTASE / glutathione dependent Formaldehyde dehydrogenase / class III alcohol dehydrogenase / MAD | ||||||
Function / homology | Function and homology information formaldehyde dehydrogenase (NAD+) activity / S-(hydroxymethyl)glutathione dehydrogenase (NADP+) activity / S-(hydroxymethyl)glutathione dehydrogenase (NAD+) activity / S-(hydroxymethyl)glutathione dehydrogenase / fatty acid omega-oxidation / S-(hydroxymethyl)glutathione dehydrogenase [NAD(P)+] activity / formaldehyde catabolic process / response to nitrosative stress / Ethanol oxidation / respiratory system process ...formaldehyde dehydrogenase (NAD+) activity / S-(hydroxymethyl)glutathione dehydrogenase (NADP+) activity / S-(hydroxymethyl)glutathione dehydrogenase (NAD+) activity / S-(hydroxymethyl)glutathione dehydrogenase / fatty acid omega-oxidation / S-(hydroxymethyl)glutathione dehydrogenase [NAD(P)+] activity / formaldehyde catabolic process / response to nitrosative stress / Ethanol oxidation / respiratory system process / : / positive regulation of blood pressure / alcohol dehydrogenase / Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor / response to redox state / retinoid metabolic process / fatty acid binding / response to lipopolysaccharide / electron transfer activity / mitochondrion / zinc ion binding / extracellular exosome / identical protein binding / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.2 Å | ||||||
Authors | Sanghani, P.C. / Robinson, H. / Hurley, T.D. / Bosron, W.F. | ||||||
Citation | Journal: Chem.Biol.Interact. / Year: 2003 Title: Structure-function relationships in human Class III alcohol dehydrogenase (formaldehyde dehydrogenase) Authors: Sanghani, P.C. / Robinson, H. / Bennett-Lovsey, R. / Hurley, T.D. / Bosron, W.F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1mp0.cif.gz | 167.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1mp0.ent.gz | 131.8 KB | Display | PDB format |
PDBx/mmJSON format | 1mp0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1mp0_validation.pdf.gz | 982.9 KB | Display | wwPDB validaton report |
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Full document | 1mp0_full_validation.pdf.gz | 991.7 KB | Display | |
Data in XML | 1mp0_validation.xml.gz | 36.1 KB | Display | |
Data in CIF | 1mp0_validation.cif.gz | 53.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mp/1mp0 ftp://data.pdbj.org/pub/pdb/validation_reports/mp/1mp0 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 39641.000 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ADH5 / Plasmid: pKK223-3 / Production host: Escherichia coli (E. coli) / Strain (production host): TG-1 References: UniProt: P11766, alcohol dehydrogenase, EC: 1.2.1.1 |
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-Non-polymers , 5 types, 693 molecules
#2: Chemical | ChemComp-ZN / #3: Chemical | #4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
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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: 3.07 Å3/Da / Density % sol: 59.92 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.9 Details: PEG8000, Potassium phosphate, Zinc sulphate, Dithiothreitol, pH 6.9, VAPOR DIFFUSION, SITTING DROP, temperature 277K | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7.1 | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X12B / Wavelength: 1.2836, 1.2835, 1.2652 | ||||||||||||
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 23, 2001 | ||||||||||||
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2.2→20 Å / Num. all: 51598 / Num. obs: 46219 / % possible obs: 89.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 22 % / Biso Wilson estimate: 17.2 Å2 / Rmerge(I) obs: 0.056 / Net I/σ(I): 52.5 | ||||||||||||
Reflection shell | Resolution: 2.2→2.28 Å / Redundancy: 11.3 % / Rmerge(I) obs: 0.354 / Mean I/σ(I) obs: 6.9 / Num. unique all: 2620 / % possible all: 52.2 | ||||||||||||
Reflection | *PLUS Lowest resolution: 20 Å | ||||||||||||
Reflection shell | *PLUS % possible obs: 52.2 % |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.2→19.9 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 3128187.44 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 34.8761 Å2 / ksol: 0.355188 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.2→19.9 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: CONSTR | ||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.2→2.28 Å / Rfactor Rfree error: 0.027 / Total num. of bins used: 10
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Xplor file |
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Refinement | *PLUS Rfactor Rfree: 0.2182 / Rfactor Rwork: 0.1894 | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.29 |