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Yorodumi- PDB-9xia: X-RAY ANALYSIS OF D-XYLOSE ISOMERASE AT 1.9 ANGSTROMS: NATIVE ENZ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 9xia | |||||||||
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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 | |||||||||
Components | XYLOSE ISOMERASE | |||||||||
Keywords | ISOMERASE(INTRAMOLECULAR OXIDOREDUCTASE) | |||||||||
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 / Resolution: 1.9 Å | |||||||||
Authors | Carrell, H.L. / Glusker, J.P. | |||||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 1989 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: Journal: Protein Eng. / Year: 1987 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: Journal: J.Biol.Chem. / Year: 1984 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. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 9xia.cif.gz | 91.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb9xia.ent.gz | 71.3 KB | Display | PDB format |
PDBx/mmJSON format | 9xia.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xi/9xia ftp://data.pdbj.org/pub/pdb/validation_reports/xi/9xia | HTTPS FTP |
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-Related structure data
-Links
-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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Details | 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. |
-Components
#1: Protein | Mass: 43254.234 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces rubiginosus (bacteria) / References: UniProt: P24300, xylose isomerase | ||||
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#2: Sugar | ChemComp-DFR / | ||||
#3: Chemical | #4: Water | ChemComp-HOH / | Sequence details | THE AMINO ACID SEQUENCE WAS TAKEN FROM INTERNATIONAL PATENT APPLICATION NUMBER:PCT/US88/02765, ...THE AMINO ACID SEQUENCE WAS TAKEN FROM INTERNATIO | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.79 Å3/Da / Density % sol: 55.93 % | ||||||||||||||||||||
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Crystal grow | *PLUS Temperature: 4 ℃ / pH: 7.4 / Method: batch method | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Radiation | Scattering type: x-ray |
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Radiation wavelength | Relative weight: 1 |
Reflection | *PLUS Highest resolution: 1.9 Å / Num. obs: 36274 / % possible obs: 94 % / Num. measured all: 71368 / Biso Wilson estimate: 22 Å2 |
-Processing
Software | Name: PROLSQ / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Resolution: 1.9→8 Å /
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Refinement step | Cycle: LAST / Resolution: 1.9→8 Å
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Refine LS restraints |
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Software | *PLUS Name: PROLSQ / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 1.9 Å / Lowest resolution: 8 Å / Num. reflection obs: 30250 / σ(I): 1.5 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 17 Å2 |