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Yorodumi- PDB-5zci: Crystal structure of apo form of Xylose reductase from Debaryomyc... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5zci | ||||||
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Title | Crystal structure of apo form of Xylose reductase from Debaryomyces nepalensis | ||||||
Components | Aldose reductase | ||||||
Keywords | OXIDOREDUCTASE / carbohydrate metabolism / aldo-keto reductase / TIM barrel / NADPH dependent | ||||||
Function / homology | Function and homology information D-xylose reductase [NAD(P)H] / D-xylose reductase (NADPH) activity / D-xylose catabolic process Similarity search - Function | ||||||
Biological species | Debaryomyces nepalensis (yeast) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Manoj, N. | ||||||
Citation | Journal: FEBS J. / Year: 2018 Title: Crystal structure of yeast xylose reductase in complex with a novel NADP-DTT adduct provides insights into substrate recognition and catalysis. Authors: Paidimuddala, B. / Mohapatra, S.B. / Gummadi, S.N. / Manoj, N. #1: Journal: RSC Adv. / Year: 2017 Title: A halotolerant aldose reductase from Debaryomyces nepalensis: gene isolation, overexpression and biochemical characterization Authors: Paidimuddala, B. / Aradhyam, G.K. / Gummadi, S.N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5zci.cif.gz | 246.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5zci.ent.gz | 197.5 KB | Display | PDB format |
PDBx/mmJSON format | 5zci.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zc/5zci ftp://data.pdbj.org/pub/pdb/validation_reports/zc/5zci | HTTPS FTP |
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-Related structure data
Related structure data | 5zcmC 1jezS 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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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 38920.312 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Debaryomyces nepalensis (yeast) / Gene: AR / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Variant (production host): Rosetta / References: UniProt: A0A0M4HL56, aldose reductase #2: 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: 2.2 Å3/Da / Density % sol: 44.1 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.2 Details: 24% PEG 3000, 0.1 M sodium citrate (pH 6.2), 0.15 M ammonium acetate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Feb 3, 2016 |
Radiation | Monochromator: double mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2→52.4 Å / Num. obs: 42060 / % possible obs: 89.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.5 % / Biso Wilson estimate: 25.9 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.157 / Rpim(I) all: 0.049 / Rrim(I) all: 0.165 / Net I/σ(I): 12.6 |
Reflection shell | Resolution: 2→2.11 Å / Redundancy: 10.7 % / Rmerge(I) obs: 0.745 / Mean I/σ(I) obs: 3.1 / Num. unique obs: 5483 / CC1/2: 0.779 / Rpim(I) all: 0.232 / Rrim(I) all: 0.781 / % possible all: 81.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1JEZ Resolution: 2→48.857 Å / SU ML: 0.22 / SU R Cruickshank DPI: 0.224 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.74
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.2 Å2 | ||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.238 Å / Luzzati d res low obs: 48.9 Å | ||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→48.857 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.047 Å
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