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Yorodumi- PDB-3kbn: Room temperature structure of D-Xylose Isomerase in complex with ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3kbn | ||||||
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Title | Room temperature structure of D-Xylose Isomerase in complex with 2Ni(2+) co-factors and d12-D-glucose in the linear form | ||||||
Components | Xylose isomerase | ||||||
Keywords | ISOMERASE / xylose isomerase / linear D-glucose / Carbohydrate metabolism / Metal-binding / Pentose shunt / Xylose metabolism | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 1.53 Å | ||||||
Authors | Kovalevsky, A.Y. / Hanson, L. / Langan, P. | ||||||
Citation | Journal: Structure / Year: 2010 Title: Metal ion roles and the movement of hydrogen during reaction catalyzed by D-xylose isomerase: a joint x-ray and neutron diffraction study. Authors: Kovalevsky, A.Y. / Hanson, L. / Fisher, S.Z. / Mustyakimov, M. / Mason, S.A. / Forsyth, V.T. / Blakeley, M.P. / Keen, D.A. / Wagner, T. / Carrell, H.L. / Katz, A.K. / Glusker, J.P. / Langan, P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3kbn.cif.gz | 182.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3kbn.ent.gz | 143.7 KB | Display | PDB format |
PDBx/mmJSON format | 3kbn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3kbn_validation.pdf.gz | 445.4 KB | Display | wwPDB validaton report |
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Full document | 3kbn_full_validation.pdf.gz | 450.9 KB | Display | |
Data in XML | 3kbn_validation.xml.gz | 20.1 KB | Display | |
Data in CIF | 3kbn_validation.cif.gz | 30.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kb/3kbn ftp://data.pdbj.org/pub/pdb/validation_reports/kb/3kbn | HTTPS FTP |
-Related structure data
Related structure data | 3kbmC 3kbsC 3kbvC 3kbwC 3kclC 3kcoC 1xibS C: citing same article (ref.) S: Starting model for refinement |
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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 genetically manipulated source Details: THE PROTEIN WAS PURCHASED FROM HAMPTON RESEARCH / Source: (gene. exp.) Streptomyces rubiginosus (bacteria) / Gene: xylA / References: UniProt: P24300, xylose isomerase | ||||||
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#2: Chemical | #3: Sugar | ChemComp-GLO / | #4: Water | ChemComp-HOH / | Source details | THE PROTEIN WAS PURCHASED FROM HAMPTON RESEARCH | |
-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: 55.81 % |
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Crystal grow | Temperature: 290 K / pH: 7.7 Details: 40mg/ml protein, 5mM NiCl2, 500mM d12-D-glucose 30% (v/v) ammonium sulfate (sat.), pH 7.7, temperature 290K |
-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-E DW / Wavelength: 1.54 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Mar 10, 2009 |
Radiation | Monochromator: Varimax mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 1.53→20 Å / Num. all: 72268 / Num. obs: 61655 / % possible obs: 85 % / Observed criterion σ(F): 4 / Observed criterion σ(I): 2 |
Reflection shell | Resolution: 1.53→1.58 Å / % possible all: 93.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1XIB Resolution: 1.53→20 Å / Num. parameters: 30754 / Num. restraintsaints: 37993 / 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: 3360.5 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.53→20 Å
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Refine LS restraints |
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