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Yorodumi- PDB-4qeh: Room temperature X-ray structure of D-xylose isomerase in complex... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4qeh | |||||||||
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Title | Room temperature X-ray structure of D-xylose isomerase in complex with two Mg2+ ions and L-ribose | |||||||||
Components | Xylose isomerase | |||||||||
Keywords | ISOMERASE / TIM barrel / sugar isomerase / monosaccharides | |||||||||
Function / homology | Function and homology information xylose isomerase / D-xylose metabolic process / xylose isomerase activity / magnesium ion binding / identical protein binding / cytoplasm Similarity search - Function | |||||||||
Biological species | Streptomyces rubiginosus (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / AB INITIO / Resolution: 1.55 Å | |||||||||
Authors | Kovalevsky, A.Y. / Langan, P. | |||||||||
Citation | Journal: Structure / Year: 2014 Title: L-Arabinose Binding, Isomerization, and Epimerization by D-Xylose Isomerase: X-Ray/Neutron Crystallographic and Molecular Simulation Study. Authors: Langan, P. / Sangha, A.K. / Wymore, T. / Parks, J.M. / Yang, Z.K. / Hanson, B.L. / Fisher, Z. / Mason, S.A. / Blakeley, M.P. / Forsyth, V.T. / Glusker, J.P. / Carrell, H.L. / Smith, J.C. / ...Authors: Langan, P. / Sangha, A.K. / Wymore, T. / Parks, J.M. / Yang, Z.K. / Hanson, B.L. / Fisher, Z. / Mason, S.A. / Blakeley, M.P. / Forsyth, V.T. / Glusker, J.P. / Carrell, H.L. / Smith, J.C. / Keen, D.A. / Graham, D.E. / Kovalevsky, A. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4qeh.cif.gz | 95.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4qeh.ent.gz | 71.4 KB | Display | PDB format |
PDBx/mmJSON format | 4qeh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4qeh_validation.pdf.gz | 437.1 KB | Display | wwPDB validaton report |
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Full document | 4qeh_full_validation.pdf.gz | 440.9 KB | Display | |
Data in XML | 4qeh_validation.xml.gz | 18.1 KB | Display | |
Data in CIF | 4qeh_validation.cif.gz | 27.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qe/4qeh ftp://data.pdbj.org/pub/pdb/validation_reports/qe/4qeh | HTTPS FTP |
-Related structure data
Related structure data | 4qdpC 4qdwC 4qe1C 4qe4C 4qe5C 4qeeC 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: 43283.297 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Streptomyces rubiginosus (bacteria) / References: UniProt: P24300, xylose isomerase | ||||
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#2: Chemical | #3: Sugar | ChemComp-32O / | #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: 2.78 Å3/Da / Density % sol: 55.8 % |
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Crystal grow | Temperature: 291 K / Method: batch / pH: 7.7 Details: 30% ammonium sulfate, 0.1M HEPES pH 7.7, batch, temperature 291K |
-Data collection
Diffraction | Mean temperature: 291 K |
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Diffraction source | Source: ROTATING ANODE / Wavelength: 1.54 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Mar 15, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 1.55→40 Å / Num. all: 69155 / Num. obs: 58816 / % possible obs: 85 % / Observed criterion σ(F): 4 / Observed criterion σ(I): 2 |
-Processing
Software |
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Refinement | Method to determine structure: AB INITIO Starting model: NONE Resolution: 1.55→20 Å / Num. parameters: 13395 / Num. restraintsaints: 12758 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
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Refine analyze | Num. disordered residues: 5 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 3316.5 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.55→20 Å
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Refine LS restraints |
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