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Yorodumi- PDB-6t8e: Crystal structure of native xylose isomerase from Piromyces E2 gr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6t8e | |||||||||
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Title | Crystal structure of native xylose isomerase from Piromyces E2 grown in yeast, in complex with xylose | |||||||||
Components | Xylose isomerase | |||||||||
Keywords | ISOMERASE / TIM-barrel | |||||||||
Function / homology | Function and homology information xylose catabolic process to ethanol / xylose isomerase / xylose isomerase activity / metal ion binding / cytoplasm Similarity search - Function | |||||||||
Biological species | Piromyces sp. | |||||||||
Method | X-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 1.86 Å | |||||||||
Authors | Rozeboom, H.J. / Janssen, D.B. | |||||||||
Citation | Journal: Biotechnol Biofuels / Year: 2020 Title: Structure-based directed evolution improves S. cerevisiae growth on xylose by influencing in vivo enzyme performance. Authors: Lee, M. / Rozeboom, H.J. / Keuning, E. / de Waal, P. / Janssen, D.B. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6t8e.cif.gz | 712.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6t8e.ent.gz | 587.6 KB | Display | PDB format |
PDBx/mmJSON format | 6t8e.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/t8/6t8e ftp://data.pdbj.org/pub/pdb/validation_reports/t8/6t8e | HTTPS FTP |
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-Related structure data
Related structure data | 6t8fC 5nh5S 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
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 49458.672 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Piromyces sp. (strain E2) (fungus) / Strain: E2 / Gene: xylA / Production host: Saccharomyces cerevisiae (brewer's yeast) / Strain (production host): DS75543 / References: UniProt: Q9P8C9, xylose isomerase |
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-Sugars , 3 types, 22 molecules
#3: Sugar | ChemComp-XLS / #4: Sugar | ChemComp-XYP / #5: Sugar | ChemComp-XYS / |
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-Non-polymers , 3 types, 1922 molecules
#2: Chemical | ChemComp-CA / #6: Chemical | ChemComp-SO4 / #7: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | N |
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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: 2.3 Å3/Da / Density % sol: 45 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 14-17 % PEG3350, HEPES, pH 7 |
-Data collection
Diffraction | Mean temperature: 110 K / Serial crystal experiment: N |
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Diffraction source | Source: ROTATING ANODE / Type: BRUKER AXS MICROSTAR-H / Wavelength: 1.54 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 27, 2018 |
Radiation | Monochromator: HELIOS MX Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 1.86→46.6 Å / Num. obs: 135735 / % possible obs: 93.6 % / Redundancy: 2.1 % / CC1/2: 0.931 / Rmerge(I) obs: 0.066 / Rpim(I) all: 0.06 / Rrim(I) all: 0.09 / Net I/σ(I): 7.1 |
Reflection shell | Resolution: 1.86→1.89 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.38 / Num. unique obs: 5669 / CC1/2: 0.286 / Rpim(I) all: 0.35 / Rrim(I) all: 0.518 / % possible all: 79.1 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 5NH5 Resolution: 1.86→46.6 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.949 / SU B: 5.711 / SU ML: 0.088 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.134 / ESU R Free: 0.12 Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: 65.52 Å2 / Biso mean: 18.438 Å2 / Biso min: 6.64 Å2
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Refinement step | Cycle: final / Resolution: 1.86→46.6 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.86→1.909 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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