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Yorodumi- PDB-3kco: Room temperature neutron structure of D-Xylose Isomerase in compl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3kco | ||||||
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Title | Room temperature neutron structure of D-Xylose Isomerase in complex with two Ni2+ cations and d12-D-glucose in the linear form (refined jointly with X-ray structure 3KBN) | ||||||
Components | Xylose isomerase | ||||||
Keywords | ISOMERASE / xylose isomerase / deuterated 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 | NEUTRON DIFFRACTION / X-RAY DIFFRACTION / NUCLEAR REACTOR / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Kovalevsky, A.Y. / 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 | 3kco.cif.gz | 174.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3kco.ent.gz | 141.8 KB | Display | PDB format |
PDBx/mmJSON format | 3kco.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3kco_validation.pdf.gz | 423.3 KB | Display | wwPDB validaton report |
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Full document | 3kco_full_validation.pdf.gz | 424 KB | Display | |
Data in XML | 3kco_validation.xml.gz | 9.8 KB | Display | |
Data in CIF | 3kco_validation.cif.gz | 15.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kc/3kco ftp://data.pdbj.org/pub/pdb/validation_reports/kc/3kco | HTTPS FTP |
-Related structure data
Related structure data | 3kbmC 3kbnC 3kbsC 3kbvC 3kbwC 3kclC 3cwhS 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: Chemical | ChemComp-DOD / | Source details | THE PROTEIN WAS PURCHASED FROM HAMPTON RESEARCH | |
-Experimental details
-Experiment
Experiment |
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-Sample preparation
Crystal | Density Matthews: 2.78 Å3/Da / Density % sol: 55.81 % |
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Crystal grow | Temperature: 293 K / pH: 7.7 Details: 50MM HEPES, 40% v/v (NH4)2SO4 (sat.), protein 40 MG/ML, PH=7.7, BATCH METHOD, APO-XI CRYSTALS WERE SOAKED WITH 5mM NiCl2 SALT, 0.5M PER-DEUTERATED D-GLUCOSE IN D2O, temperature 293K |
-Data collection
Diffraction |
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Diffraction source |
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Detector |
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Radiation |
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Radiation wavelength |
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Reflection | Resolution: 1.8→20 Å / Num. all: 37568 / Num. obs: 27031 / % possible obs: 72 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 1.7 / Redundancy: 3.2 % / Rsym value: 0.236 / Net I/σ(I): 4 | |||||||||||||||
Reflection shell | Resolution: 1.8→1.9 Å / Redundancy: 1.9 % / Mean I/σ(I) obs: 1.5 / Rsym value: 0.359 / % possible all: 72.5 |
-Processing
Software |
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Refinement | % reflection Rfree: 5.1 % / R Free selection details: RANDOM / σ(F): 3 / Method to determine structure: MOLECULAR REPLACEMENT / Starting model: 3CWH
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Refinement step | Cycle: LAST / Resolution: 1.8→20 Å
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Refine LS restraints |
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