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Yorodumi- PDB-5nhe: Crystal structure of xylose isomerase from Piromyces E2 in comple... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5nhe | |||||||||
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Title | Crystal structure of xylose isomerase from Piromyces E2 in complex with two Cd2+ ions and xylose | |||||||||
Components | Xylose isomerase | |||||||||
Keywords | ISOMERASE / TIM-barrel | |||||||||
Function / homology | Function and homology information D-xylose catabolic process to ethanol / xylose isomerase / xylose isomerase activity / metal ion binding / cytoplasm Similarity search - Function | |||||||||
Biological species | Piromyces sp. E2 (fungus) | |||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.86 Å | |||||||||
Authors | Rozeboom, H.J. / Janssen, D.B. | |||||||||
Citation | Journal: Biochemistry / Year: 2017 Title: Metal Dependence of the Xylose Isomerase from Piromyces sp. E2 Explored by Activity Profiling and Protein Crystallography. Authors: Lee, M. / Rozeboom, H.J. / de Waal, P.P. / de Jong, R.M. / Dudek, H.M. / 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 | 5nhe.cif.gz | 714.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5nhe.ent.gz | 590.5 KB | Display | PDB format |
PDBx/mmJSON format | 5nhe.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5nhe_validation.pdf.gz | 509 KB | Display | wwPDB validaton report |
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Full document | 5nhe_full_validation.pdf.gz | 520.6 KB | Display | |
Data in XML | 5nhe_validation.xml.gz | 79.5 KB | Display | |
Data in CIF | 5nhe_validation.cif.gz | 121.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nh/5nhe ftp://data.pdbj.org/pub/pdb/validation_reports/nh/5nhe | HTTPS FTP |
-Related structure data
Related structure data | 5nh4C 5nh5C 5nh6C 5nh7C 5nh8C 5nh9C 5nhaC 5nhbC 5nhcC 5nhdC 5nhmC C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: GLN / End label comp-ID: GLN / Refine code: _ / Auth seq-ID: 2 - 437 / Label seq-ID: 2 - 437
NCS ensembles :
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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. E2 (fungus) / Gene: xylA Details (production host): pBR322 ori and ampicillin resistance gene Production host: Escherichia coli K-12 (bacteria) / Variant (production host): TOP10 or Neb10-beta / References: UniProt: Q9P8C9, xylose isomerase |
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-Sugars , 3 types, 16 molecules
#3: Sugar | #4: Sugar | ChemComp-XYP / #5: Sugar | ChemComp-XYS / |
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-Non-polymers , 3 types, 1853 molecules
#2: Chemical | ChemComp-CD / #6: Chemical | ChemComp-SO4 / #7: 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: 2.3 Å3/Da / Density % sol: 45 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 13-15 % PEG3350, 0.1 mM CdCl2, 0.1 M Hepes pH 7.0 |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: ROTATING ANODE / Type: BRUKER AXS MICROSTAR-H / Wavelength: 1.5418 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 27, 2014 |
Radiation | Monochromator: Helios MX mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.86→45.1 Å / Num. obs: 128136 / % possible obs: 87.8 % / Redundancy: 2 % / Biso Wilson estimate: 9.4 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.063 / Rpim(I) all: 0.059 / Net I/σ(I): 9.4 |
Reflection shell | Resolution: 1.86→1.89 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.386 / Mean I/σ(I) obs: 2 / Num. unique obs: 4052 / CC1/2: 0.644 / Rpim(I) all: 0.361 / % possible all: 55.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: D_1200004044 Resolution: 1.86→45.1 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.955 / SU B: 5.083 / SU ML: 0.08 / Cross valid method: THROUGHOUT / ESU R: 0.146 / ESU R Free: 0.118 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.651 Å2
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Refinement step | Cycle: 1 / Resolution: 1.86→45.1 Å
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Refine LS restraints |
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