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- PDB-3kbm: Room Temperature X-ray structure of D-Xylose Isomerase complexed ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3kbm | ||||||
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Title | Room Temperature X-ray structure of D-Xylose Isomerase complexed with 2Cd(2+) co-factors and d12-D-alpha-glucose in the cyclic form | ||||||
![]() | Xylose isomerase![]() | ||||||
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Function / homology | ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Kovalevsky, A.Y. / Hanson, L. / Langan, P. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 96.3 KB | Display | ![]() |
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PDB format | ![]() | 71.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3kbnC ![]() 3kbsC ![]() 3kbvC ![]() 3kbwC ![]() 3kclC ![]() 3kcoC ![]() 1xibS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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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.) ![]() ![]() ![]() | ||||||
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#2: Chemical | #3: Sugar | ChemComp-GLC / | ![]() #4: Water | ChemComp-HOH / | ![]() Source details | THE PROTEIN WAS PURCHASED FROM HAMPTON RESEARCH | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.79 Å3/Da / Density % sol: 55.84 % |
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Crystal grow![]() | Temperature: 290 K / pH: 7.7 Details: 40mg/ml protein, 5mM CdCl2; 500mM d12-D-glucose, 30% (v/v) ammonium sulfate (sat.), batch, pH 7.7, temperature 290K |
-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jan 15, 2009 / Details: Varimax mirrors |
Radiation | Monochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2→20 Å / Num. all: 30084 / Num. obs: 27223 / % possible obs: 90 % / Observed criterion σ(F): 4 / Observed criterion σ(I): 2 |
Reflection shell | Resolution: 2→2.07 Å / % possible all: 93.3 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 1XIB Resolution: 2→20 Å / Num. parameters: 13197 / Num. restraintsaints: 12700 / 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: 3259 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→20 Å
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Refine LS restraints |
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