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- PDB-8xia: X-RAY ANALYSIS OF D-XYLOSE ISOMERASE AT 1.9 ANGSTROMS: NATIVE ENZ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8xia | ||||||
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Title | X-RAY ANALYSIS OF D-XYLOSE ISOMERASE AT 1.9 ANGSTROMS: NATIVE ENZYME IN COMPLEX WITH SUBSTRATE AND WITH A MECHANISM-DESIGNED INACTIVATOR | ||||||
![]() | XYLOSE ISOMERASE | ||||||
![]() | ISOMERASE(INTRAMOLECULAR OXIDOREDUCTASE) | ||||||
Function / homology | ![]() xylose isomerase / D-xylose metabolic process / xylose isomerase activity / magnesium ion binding / identical protein binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() | ||||||
![]() | Carrell, H.L. / Glusker, J.P. | ||||||
![]() | ![]() Title: X-ray analysis of D-xylose isomerase at 1.9 A: native enzyme in complex with substrate and with a mechanism-designed inactivator. Authors: Carrell, H.L. / Glusker, J.P. / Burger, V. / Manfre, F. / Tritsch, D. / Biellmann, J.F. #1: ![]() Title: Comparison of Backbone Structures of Glucose Isomerase from Streptomyces and Arthrobacter Authors: Henrick, K. / Blow, D.M. / Carrell, H.L. / Glusker, J.P. #2: ![]() Title: X-Ray Crystal Structure of D-Xylose Isomerase at 4-Angstroms Resolution Authors: Carrell, H.L. / Rubin, B.H. / Hurley, T.J. / Glusker, J.P. | ||||||
History |
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Remark 700 | SHEET THE STRUCTURE OF THE MONOMER IS AN EIGHT-FOLD ALPHA-BETA BARREL WITH AN EXTENDED C-TERMINAL ...SHEET THE STRUCTURE OF THE MONOMER IS AN EIGHT-FOLD ALPHA-BETA BARREL WITH AN EXTENDED C-TERMINAL LOOP WHICH FACILITATES AGGREGATION OF MONOMERS TO TETRAMERS. TETRAMERS ARE POSITIONED ON THE 222 SYMMETRY SITE AT THE ORIGIN OF THE CELL. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 95.7 KB | Display | ![]() |
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PDB format | ![]() | 72.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 384.9 KB | Display | ![]() |
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Full document | ![]() | 397.3 KB | Display | |
Data in XML | ![]() | 10.7 KB | Display | |
Data in CIF | ![]() | 17.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related 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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Atom site foot note | 1: RESIDUE PRO 187 IS A CIS PROLINE. | |||||||||
Components on special symmetry positions |
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Components
#1: Protein | Mass: 43254.234 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() | ||||
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#2: Sugar | ChemComp-XLS / | ||||
#3: Chemical | #4: Water | ChemComp-HOH / | Nonpolymer details | THE SUBSTRATE D-XYLOSE IS IN AN EXTENDED CONFORMATION AND APPEARS TO BE A MIXTURE OF D-XYLULOSE AND ...THE SUBSTRATE D-XYLOSE IS IN AN EXTENDED CONFORMATI | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.81 Å3/Da / Density % sol: 56.29 % | ||||||||||||||||||||||||
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Crystal grow | *PLUS pH: 7.4 / Method: unknown | ||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Reflection | *PLUS Highest resolution: 1.9 Å / Num. obs: 38364 / % possible obs: 98 % / Observed criterion σ(I): 1.5 / Rmerge(I) obs: 0.141 |
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Processing
Software | Name: PROLSQ / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Resolution: 1.9→8 Å / σ(I): 1.5 /
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Refinement step | Cycle: LAST / Resolution: 1.9→8 Å
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Refine LS restraints |
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Refinement | *PLUS Highest resolution: 1.9 Å / Lowest resolution: 8 Å / Num. reflection obs: 30656 / σ(I): 1.5 / Rfactor obs: 0.14 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |