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Yorodumi- PDB-3kbw: Room temperature X-ray mixed-metal structure of D-Xylose Isomeras... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3kbw | ||||||
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Title | Room temperature X-ray mixed-metal structure of D-Xylose Isomerase in complex with Ni(2+) and Mg(2+) co-factors | ||||||
Components | Xylose isomerase | ||||||
Keywords | ISOMERASE / xylose isomerase / 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 / AB INITIO / Resolution: 1.6 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 | 3kbw.cif.gz | 179.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3kbw.ent.gz | 142.2 KB | Display | PDB format |
PDBx/mmJSON format | 3kbw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3kbw_validation.pdf.gz | 425.8 KB | Display | wwPDB validaton report |
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Full document | 3kbw_full_validation.pdf.gz | 431.2 KB | Display | |
Data in XML | 3kbw_validation.xml.gz | 18.9 KB | Display | |
Data in CIF | 3kbw_validation.cif.gz | 28.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kb/3kbw ftp://data.pdbj.org/pub/pdb/validation_reports/kb/3kbw | HTTPS FTP |
-Related structure data
Related structure data | 3kbmC 3kbnC 3kbsC 3kbvC 3kclC 3kcoC 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 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 | ChemComp-NI / |
#3: Chemical | ChemComp-MG / |
#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: 55.8 % |
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Crystal grow | Temperature: 290 K / Method: batch / pH: 7.7 Details: 40mg/ml protein, 2mM NiCl2, 2mM MgCl2, 30% (v/v) ammonium sulfate (sat.), pH 7.7, batch, temperature 290K |
-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: ROTATING ANODE / Wavelength: 1.54 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Aug 26, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→10 Å / Num. all: 62867 / Num. obs: 50014 / % possible obs: 80 % / Observed criterion σ(F): 4 / Observed criterion σ(I): 2 |
Reflection shell | Resolution: 1.6→1.65 Å / % possible all: 95 |
-Processing
Software |
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Refinement | Method to determine structure: AB INITIO / Resolution: 1.6→10 Å / Num. parameters: 30463 / Num. restraintsaints: 37750 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
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Refine analyze | Num. disordered residues: 3 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 3338 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.6→10 Å
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Refine LS restraints |
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