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Yorodumi- PDB-5z6u: Crystal structure of D-xylose reductase from Scheffersomyces stipitis -
+Open data
-Basic information
Entry | Database: PDB / ID: 5z6u | ||||||
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Title | Crystal structure of D-xylose reductase from Scheffersomyces stipitis | ||||||
Components | NAD(P)H-dependent D-xylose reductase | ||||||
Keywords | OXIDOREDUCTASE / Pontose metabolism / xylose reductase / Scheffersomyces stipitis | ||||||
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 | Scheffersomyces stipitis (fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å | ||||||
Authors | Son, H.F. / Kim, K.J. | ||||||
Citation | Journal: Sci Rep / Year: 2018 Title: Structural insight intoD-xylose utilization by xylose reductase from Scheffersomyces stipitis. Authors: Son, H.F. / Lee, S.M. / Kim, K.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5z6u.cif.gz | 147.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5z6u.ent.gz | 114.2 KB | Display | PDB format |
PDBx/mmJSON format | 5z6u.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5z6u_validation.pdf.gz | 454.5 KB | Display | wwPDB validaton report |
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Full document | 5z6u_full_validation.pdf.gz | 460.6 KB | Display | |
Data in XML | 5z6u_validation.xml.gz | 28.3 KB | Display | |
Data in CIF | 5z6u_validation.cif.gz | 41.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z6/5z6u ftp://data.pdbj.org/pub/pdb/validation_reports/z6/5z6u | HTTPS FTP |
-Related structure data
Related structure data | 5z6tC 1z9aS 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 39135.328 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Scheffersomyces stipitis (strain ATCC 58785 / CBS 6054 / NBRC 10063 / NRRL Y-11545) (fungus) Strain: ATCC 58785 / CBS 6054 / NBRC 10063 / NRRL Y-11545 / Gene: XYL1, PICST_89614 / Plasmid: pProEX-HTa / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): T1R / References: UniProt: P31867, D-xylose reductase [NAD(P)H] #2: Chemical | #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: 2.57 Å3/Da / Density % sol: 52.18 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: PEG 3350, Ammonium citrate tribasic |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.97934 Å |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: May 10, 2017 |
Radiation | Monochromator: Double Crystal Monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97934 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→71.04 Å / Num. obs: 51177 / % possible obs: 98.8 % / Redundancy: 6.7 % / Rsym value: 0.208 / Net I/σ(I): 55.2 |
Reflection shell | Resolution: 1.95→1.98 Å / Num. unique obs: 2698 / Rsym value: 0.208 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1Z9A Resolution: 1.95→71.04 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.935 / SU B: 3.595 / SU ML: 0.104 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.163 / ESU R Free: 0.154 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 93.79 Å2 / Biso mean: 36.514 Å2 / Biso min: 19.97 Å2
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Refinement step | Cycle: final / Resolution: 1.95→71.04 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.951→2.001 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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