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Yorodumi- PDB-3gdf: Crystal structure of the NADP-dependent mannitol dehydrogenase fr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3gdf | ||||||
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Title | Crystal structure of the NADP-dependent mannitol dehydrogenase from Cladosporium herbarum. | ||||||
Components | Probable NADP-dependent mannitol dehydrogenase | ||||||
Keywords | OXIDOREDUCTASE / Rossmann fold / beta-alpha-beta motifs / open twisted sheet / Allergen / NADP | ||||||
Function / homology | Function and homology information mannitol 2-dehydrogenase (NADP+) / mannitol 2-dehydrogenase (NADP+) activity / mannitol metabolic process / oxidoreductase activity, acting on NAD(P)H, oxygen as acceptor / NADP binding / protein homotetramerization / protein homodimerization activity Similarity search - Function | ||||||
Biological species | Cladosporium herbarum (fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Nuess, D. / Goettig, P. / Magler, I. / Denk, U. / Breitenbach, M. / Schneider, P.B. / Brandstetter, H. / Simon-Nobbe, B. | ||||||
Citation | Journal: Biochimie / Year: 2010 Title: Crystal structure of the NADP-dependent mannitol dehydrogenase from Cladosporium herbarum: Implications for oligomerisation and catalysis. Authors: Nuss, D. / Goettig, P. / Magler, I. / Denk, U. / Breitenbach, M. / Schneider, P.B. / Brandstetter, H. / Simon-Nobbe, B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3gdf.cif.gz | 218.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3gdf.ent.gz | 173.6 KB | Display | PDB format |
PDBx/mmJSON format | 3gdf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3gdf_validation.pdf.gz | 443.1 KB | Display | wwPDB validaton report |
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Full document | 3gdf_full_validation.pdf.gz | 470.3 KB | Display | |
Data in XML | 3gdf_validation.xml.gz | 46.8 KB | Display | |
Data in CIF | 3gdf_validation.cif.gz | 66.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gd/3gdf ftp://data.pdbj.org/pub/pdb/validation_reports/gd/3gdf | HTTPS FTP |
-Related structure data
Related structure data | 3gdgC 1edoS 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: 28497.055 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Cladosporium herbarum (fungus) / Plasmid: pHIS-parallel2 / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21 References: UniProt: P0C0Y5, mannitol 2-dehydrogenase (NADP+) #2: Chemical | ChemComp-ZN / #3: 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: 2.14 Å3/Da / Density % sol: 42.44 % |
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Crystal grow | Temperature: 277 K / pH: 7.5 Details: 45% MPD, 0.1 M HEPES, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 1.28 |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Sep 13, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.28 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→20 Å / Num. obs: 33729 / % possible obs: 98 % / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Biso Wilson estimate: 34.6 Å2 / Rmerge(I) obs: 0.128 / Net I/σ(I): 8.6 |
Reflection shell | Resolution: 2.5→2.64 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.455 / Mean I/σ(I) obs: 2.4 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1EDO Resolution: 2.5→19.89 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 2343578.47 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 57.9 Å2 / ksol: 0.35 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.5→19.89 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.66 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
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Xplor file |
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