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Yorodumi- PDB-5zcm: Crystal structure of Xylose reductase from Debaryomyces nepalensi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5zcm | ||||||
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Title | Crystal structure of Xylose reductase from Debaryomyces nepalensis in complex with NADP-DTT adduct | ||||||
Components | Aldose reductase | ||||||
Keywords | OXIDOREDUCTASE / Carbohydrate metabolism / aldo-keto reductase / TIM barrel | ||||||
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 / molecular replacement / Resolution: 1.7 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 fromDebaryomyces 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 | 5zcm.cif.gz | 146 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5zcm.ent.gz | 112.7 KB | Display | PDB format |
PDBx/mmJSON format | 5zcm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5zcm_validation.pdf.gz | 982.1 KB | Display | wwPDB validaton report |
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Full document | 5zcm_full_validation.pdf.gz | 982.3 KB | Display | |
Data in XML | 5zcm_validation.xml.gz | 17.1 KB | Display | |
Data in CIF | 5zcm_validation.cif.gz | 25.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zc/5zcm ftp://data.pdbj.org/pub/pdb/validation_reports/zc/5zcm | HTTPS FTP |
-Related structure data
Related structure data | 5zciSC 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 38920.312 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Debaryomyces nepalensis (yeast) / Gene: AR / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3) / References: UniProt: A0A0M4HL56, aldose reductase |
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#2: Chemical | ChemComp-NDP / |
#3: Chemical | ChemComp-DTT / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.49 Å3/Da / Density % sol: 50.52 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 35% PEG 3000, 1 M HEPES (pH 7.5), 1.5 M ammonium sulfate |
-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: Jan 18, 2017 | ||||||||||||||||||||||||
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: 1.7→36.641 Å / Num. obs: 42718 / % possible obs: 99.4 % / Redundancy: 13.3 % / Biso Wilson estimate: 13.54 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.152 / Rpim(I) all: 0.043 / Rrim(I) all: 0.158 / Net I/σ(I): 13 | ||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5ZCI Resolution: 1.7→36.641 Å / SU ML: 0.18 / SU R Cruickshank DPI: 0.1143 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 16.59
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 49.86 Å2 / Biso mean: 16.92 Å2 / Biso min: 6.01 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.1646 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.7→36.641 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 15
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