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Yorodumi- PDB-2qjn: Crystal structure of D-mannonate dehydratase from Novosphingobium... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2qjn | ||||||
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Title | Crystal structure of D-mannonate dehydratase from Novosphingobium aromaticivorans complexed with Mg and 2-keto-3-deoxy-D-gluconate | ||||||
Components | Mandelate racemase/muconate lactonizing enzyme | ||||||
Keywords | LYASE / D-mannonate dehydratase / enolase superfamily | ||||||
Function / homology | Function and homology information mannonate dehydratase / mannonate dehydratase activity / amino acid catabolic process / carbohydrate catabolic process / magnesium ion binding Similarity search - Function | ||||||
Biological species | Novosphingobium aromaticivorans (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Fedorov, A.A. / Fedorov, E.V. / Rakus, J.F. / Vick, J.E. / Gerlt, J.A. / Almo, S.C. | ||||||
Citation | Journal: Biochemistry / Year: 2007 Title: Evolution of enzymatic activities in the enolase superfamily: D-Mannonate dehydratase from Novosphingobium aromaticivorans. Authors: Rakus, J.F. / Fedorov, A.A. / Fedorov, E.V. / Glasner, M.E. / Vick, J.E. / Babbitt, P.C. / Almo, S.C. / Gerlt, J.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2qjn.cif.gz | 325.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2qjn.ent.gz | 262.3 KB | Display | PDB format |
PDBx/mmJSON format | 2qjn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qj/2qjn ftp://data.pdbj.org/pub/pdb/validation_reports/qj/2qjn | HTTPS FTP |
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-Related structure data
Related structure data | 2qjjSC 2qjmC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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3 |
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Unit cell |
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Details | The biological assembly is a dimer |
-Components
#1: Protein | Mass: 45297.410 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Novosphingobium aromaticivorans (bacteria) Production host: Escherichia coli (E. coli) / References: UniProt: A4XF23 #2: Chemical | ChemComp-MG / #3: Chemical | ChemComp-KDG / #4: 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: 2.21 Å3/Da / Density % sol: 44.42 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 25% PEG 3350, 0.1M Tris, 0.2M ammonium sulfate, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97915 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 16, 2006 |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97915 Å / Relative weight: 1 |
Reflection | Resolution: 2→25 Å / Num. all: 104980 / Num. obs: 104980 / % possible obs: 96.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 17.7 Å2 / Rmerge(I) obs: 0.073 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 2QJJ Resolution: 2→24.89 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 301500.68 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 64.1996 Å2 / ksol: 0.404709 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→24.89 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.07 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 10
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Xplor file |
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