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Yorodumi- PDB-1mzr: Structure of dkga from E.coli at 2.13 A resolution solved by mole... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1mzr | ||||||
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Title | Structure of dkga from E.coli at 2.13 A resolution solved by molecular replacement | ||||||
Components | 2,5-diketo-D-gluconate reductase A | ||||||
Keywords | OXIDOREDUCTASE / alpha/beta-barrel / aldo-ketoreductase / NADPH dependant / Bacterial targets at IGS-CNRS / France / BIGS / Structural Genomics | ||||||
Function / homology | Function and homology information 2,5-didehydrogluconate reductase (2-dehydro-D-gluconate-forming) / 2,5-didehydrogluconate reductase activity / methylglyoxal catabolic process / alcohol dehydrogenase (NADP+) activity / L-ascorbic acid biosynthetic process / oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor / aldose reductase (NADPH) activity / oxidoreductase activity / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.13 Å | ||||||
Authors | Abergel, C. / Jeudy, S. / Monchois, V. / Claverie, J.M. / Bacterial targets at IGS-CNRS, France (BIGS) | ||||||
Citation | Journal: Proteins / Year: 2006 Title: Crystal structure of Escherichia coli DkgA, a broad-specificity aldo-keto reductase. Authors: Jeudy, S. / Monchois, V. / Maza, C. / Claverie, J.M. / Abergel, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1mzr.cif.gz | 134.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1mzr.ent.gz | 104.3 KB | Display | PDB format |
PDBx/mmJSON format | 1mzr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1mzr_validation.pdf.gz | 465.7 KB | Display | wwPDB validaton report |
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Full document | 1mzr_full_validation.pdf.gz | 473.2 KB | Display | |
Data in XML | 1mzr_validation.xml.gz | 28.6 KB | Display | |
Data in CIF | 1mzr_validation.cif.gz | 42.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mz/1mzr ftp://data.pdbj.org/pub/pdb/validation_reports/mz/1mzr | HTTPS FTP |
-Related structure data
Related structure data | 1a80S S: Starting model for refinement |
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Similar structure data | |
Other databases |
-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 on special symmetry positions |
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-Components
#1: Protein | Mass: 33686.398 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: yqhe / Plasmid: pDEST17 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: Q46857, Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor #2: Chemical | ChemComp-PO4 / #3: Chemical | #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: 2.99 Å3/Da / Density % sol: 58.87 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: potassium phosphate, sodium phosphate, hepes, glycerol, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 8 / Method: vapor diffusion, sitting drop | ||||||||||||||||||||||||||||||||||||||||||
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: ESRF / Beamline: ID14-2 / Wavelength: 0.934 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 15, 2001 |
Radiation | Monochromator: monochromator 0.98 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.934 Å / Relative weight: 1 |
Reflection | Resolution: 2.13→37.1 Å / Num. all: 43958 / Num. obs: 43958 / % possible obs: 96.7 % / Observed criterion σ(F): 9 / Observed criterion σ(I): 3 / Redundancy: 4.9 % / Biso Wilson estimate: 26.751 Å2 / Rmerge(I) obs: 0.075 / Rsym value: 0.075 / Net I/σ(I): 8.6 |
Reflection shell | Resolution: 2.13→2.2 Å / Redundancy: 4.8 % / Num. unique all: 4340 / Rsym value: 0.282 / % possible all: 98.3 |
Reflection | *PLUS Highest resolution: 2.16 Å / Lowest resolution: 20 Å / Num. obs: 39423 |
Reflection shell | *PLUS % possible obs: 96.7 % / Num. unique obs: 3932 / Rmerge(I) obs: 0.82 / Mean I/σ(I) obs: 2.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1A80 Resolution: 2.13→19.91 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 27 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.13→19.91 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.13→2.2 Å / Rfactor Rfree error: 0.01
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Refinement | *PLUS Rfactor obs: 0.172 / Rfactor Rfree: 0.221 / Rfactor Rwork: 0.172 / Highest resolution: 2.16 Å / Lowest resolution: 20 Å | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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