[English] 日本語
Yorodumi- PDB-3kcl: Room temperature neutron structure of D-Xylose Isomerase in compl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3kcl | ||||||
---|---|---|---|---|---|---|---|
Title | Room temperature neutron structure of D-Xylose Isomerase in complex with two Cd2+ cations and d12-D-alpha-glucose in the ring form (refined jointly with X-ray structure 3KBM) | ||||||
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: 2 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3kcl.cif.gz | 167.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3kcl.ent.gz | 136.1 KB | Display | PDB format |
PDBx/mmJSON format | 3kcl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3kcl_validation.pdf.gz | 442.4 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 3kcl_full_validation.pdf.gz | 443.9 KB | Display | |
Data in XML | 3kcl_validation.xml.gz | 17.6 KB | Display | |
Data in CIF | 3kcl_validation.cif.gz | 25.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kc/3kcl ftp://data.pdbj.org/pub/pdb/validation_reports/kc/3kcl | HTTPS FTP |
-Related structure data
Related structure data | 3kbmC 3kbnC 3kbsC 3kbvC 3kbwC 3kcoC 3cwhS C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| |||||||||
---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||
Unit cell |
| |||||||||
Components on special symmetry positions |
|
-Components
#1: Protein | Mass: 43283.297 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces rubiginosus (bacteria) / Gene: xylA / References: UniProt: P24300, xylose isomerase | ||||||
---|---|---|---|---|---|---|---|
#2: Chemical | #3: Sugar | ChemComp-GLC / | #4: Chemical | ChemComp-DOD / | Source details | THE PROTEIN WAS PURCHASED FROM HAMPTON RESEARCH | |
-Experimental details
-Experiment
Experiment |
|
---|
-Sample preparation
Crystal | Density Matthews: 2.79 Å3/Da / Density % sol: 55.84 % |
---|---|
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 WITH 5mM CDCL2 SALT, 0.5M PER-DEUTERATED D-GLUCOSE IN D2O, temperature 293K |
-Data collection
Diffraction |
| ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source |
| ||||||||||||||||||
Detector |
| ||||||||||||||||||
Radiation |
| ||||||||||||||||||
Radiation wavelength |
| ||||||||||||||||||
Reflection | Resolution: 2→20 Å / Num. all: 28961 / Num. obs: 20875 / % possible obs: 72 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1.4 | ||||||||||||||||||
Reflection shell | Resolution: 2→2.1 Å / Redundancy: 1.9 % / Mean I/σ(I) obs: 1.3 / % possible all: 76.3 |
-Processing
Software |
| |||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | σ(F): 2.5 / Method to determine structure: MOLECULAR REPLACEMENT / Starting model: 3CWH / Resolution: 2→20 Å
| |||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→20 Å
| |||||||||||||||||||||||||||
Refine LS restraints |
|