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Yorodumi- PDB-1mfz: Partially refined 2.8 A Crystal structure of GDP-mannose dehydrog... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1mfz | ||||||
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Title | Partially refined 2.8 A Crystal structure of GDP-mannose dehydrogenase from P. aeruginosa | ||||||
Components | GDP-mannose 6-dehydrogenase | ||||||
Keywords | OXIDOREDUCTASE / Rossmann fold / domain-swapped dimer / enzyme complex with cofactor and product | ||||||
Function / homology | Function and homology information GDP-mannose 6-dehydrogenase / GDP-mannose 6-dehydrogenase activity / alginic acid biosynthetic process / single-species biofilm formation / response to osmotic stress / cellular response to cell envelope stress / NAD binding Similarity search - Function | ||||||
Biological species | Pseudomonas aeruginosa (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||
Authors | Snook, C.F. / Tipton, P.A. / Beamer, L.J. | ||||||
Citation | Journal: Biochemistry / Year: 2003 Title: The crystal structure of GDP-mannose dehydrogenase: A key enzyme in alginate biosynthesis of P. aeruginosa Authors: Snook, C.F. / Tipton, P.A. / Beamer, L.J. #1: Journal: Biochemistry / Year: 2002 Title: Allosterism and cooperativity in Pseudomonas aeruginosa GDP-mannose dehydrogenase Authors: Naught, L.E. / Gilbert, S. / Imhoff, R. / Snook, C. / Beamer, L. / Tipton, P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1mfz.cif.gz | 327.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1mfz.ent.gz | 275.9 KB | Display | PDB format |
PDBx/mmJSON format | 1mfz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mf/1mfz ftp://data.pdbj.org/pub/pdb/validation_reports/mf/1mfz | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 48078.469 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: AlgD / Plasmid: pET-3a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P11759, GDP-mannose 6-dehydrogenase #2: Chemical | ChemComp-GDX / #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: 2.55 Å3/Da / Density % sol: 51.74 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 323 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: 10% PEG 3350, 20% isopropanol, 0.1 M Na citrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 323K | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7.5 | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Details: Osmic confocal |
Radiation | Monochromator: Osmic confocal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→94.691 Å / Num. obs: 48049 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Biso Wilson estimate: 34.7 Å2 / Rmerge(I) obs: 0.065 / Net I/σ(I): 16.7 |
Reflection shell | Resolution: 2.8→2.9 Å / Rmerge(I) obs: 0.217 / Mean I/σ(I) obs: 4.4 / Num. unique all: 4322 / % possible all: 90 |
Reflection | *PLUS Num. measured all: 151736 |
Reflection shell | *PLUS % possible obs: 90 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→40 Å / SU B: 14.6806 / SU ML: 0.30112 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.40486 / Stereochemistry target values: Engh & Huber
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 34.708 Å2
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Refinement step | Cycle: LAST / Resolution: 2.8→40 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.8→2.9 Å / Rfactor Rfree error: 0.35
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Refinement | *PLUS Lowest resolution: 40 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.263 / Rfactor Rwork: 0.207 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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