+Open data
-Basic information
Entry | Database: PDB / ID: 1a0c | ||||||
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Title | XYLOSE ISOMERASE FROM THERMOANAEROBACTERIUM THERMOSULFURIGENES | ||||||
Components | XYLOSE ISOMERASE | ||||||
Keywords | KETOLISOMERASE / XYLOSE METABOLISM / GLUCOSE-FRUCTOSE INTERCONVERSION / HYDRIDE TRANSFER / ALPHA-BETA BARREL / METALLOENZYME / THERMOPHILE | ||||||
Function / homology | Function and homology information xylose isomerase / D-xylose metabolic process / xylose isomerase activity / magnesium ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Thermoanaerobacterium thermosulfurigenes (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Gallay, O. / Chopra, R. / Conti, E. / Brick, P. / Blow, D. | ||||||
Citation | Journal: To be Published Title: Crystal Structures of Class II Xylose Isomerases from Two Thermophiles and a Hyperthermophile Authors: Gallay, O. / Chopra, R. / Conti, E. / Brick, P. / Jackson, R. / Hartley, B. / Vieille, C. / Zeikus, J.G. / Blow, D. #1: Journal: J.Mol.Biol. / Year: 1994 Title: Crystallization and Preliminary X-Ray Diffraction Studies of Xylose Isomerase from Thermoanaerobacterium Thermosulfurigenes Strain 4B Authors: Lloyd, L.F. / Gallay, O.S. / Akins, J. / Zeikus, J.G. #2: Journal: Biochem.J. / Year: 1991 Title: Purification and Characterization of Thermostable Glucose Isomerase from Clostridium Thermosulfurogenes and Thermoanaerobacter Strain B6A Authors: Lee, C.Y. / Zeikus, J.G. #3: Journal: J.Biol.Chem. / Year: 1990 Title: Catalytic Mechanism of Xylose (Glucose) Isomerase from Clostridium Thermosulfurogenes. Characterization of the Structural Gene and Function of Active Site Histidine Authors: Lee, C.Y. / Bagdasarian, M. / Meng, M.H. / Zeikus, J.G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1a0c.cif.gz | 365 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1a0c.ent.gz | 300.2 KB | Display | PDB format |
PDBx/mmJSON format | 1a0c.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a0/1a0c ftp://data.pdbj.org/pub/pdb/validation_reports/a0/1a0c | HTTPS FTP |
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-Related structure data
Related structure data | 1a0dC 1a0eC 6xiaS S: Starting model for refinement C: citing same article (ref.) |
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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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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
#1: Protein | Mass: 50409.691 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermoanaerobacterium thermosulfurigenes (bacteria) Strain: 4B / Cellular location: CYTOPLASM / Gene: XYLA / Plasmid: PCMG11 / Cellular location (production host): CYTOPLASM / Gene (production host): XYLA / Production host: Escherichia coli (E. coli) / Strain (production host): HB101 / References: UniProt: P19148, xylose isomerase #2: Chemical | ChemComp-CO / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.6 Å3/Da / Density % sol: 48 % Description: APPROXIMATE CELL DIMENSIONS A=85.9, B=154.0, C 159.0 WERE USED FOR SCALING AND MERGING; THE FINAL CELL DIMENSIONS WERE OBTAINED FROM POST-REFINEMENT. |
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Crystal grow | pH: 6 Details: PROTEIN IN 50 MM MOPS, 10 MM MGSO4, 1 MM COCL2, PH 7.0, WAS CRYSTALLIZED FROM 12% JEFFAMINE ED 4000, 50 MM MES, PH 6.0 (FOR DETAILS SEE REFERENCE 1). PH range: 6.0-7.0 |
-Data collection
Diffraction | Mean temperature: 278 K |
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Diffraction source | Source: SYNCHROTRON / Site: SRS / Beamline: PX9.5 / Wavelength: 1 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 1, 1993 / Details: MIRRORS |
Radiation | Monochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→10 Å / Num. obs: 61292 / % possible obs: 83.6 % / Redundancy: 2.1 % / Biso Wilson estimate: 30.6 Å2 / Rmerge(I) obs: 0.084 / Net I/σ(I): 7.6 |
Reflection shell | Resolution: 2.5→2.63 Å / Redundancy: 2 % / Rmerge(I) obs: 0.185 / Mean I/σ(I) obs: 3.8 / % possible all: 73.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 6XIA Resolution: 2.5→10 Å / Rfactor Rfree error: 0.003 / Cross valid method: A POSTERIORI Details: SOME DISORDERED SIDE CHAINS WERE NOT INCLUDED IN REFINEMENT. SOLVENT MOLECULES HOH 776, HOH 777, HOH 778 AND HOH 779 WERE NOT INCLUDED IN REFINEMENT SINCE THEY LIE ON OR NEAR TO NON- ...Details: SOME DISORDERED SIDE CHAINS WERE NOT INCLUDED IN REFINEMENT. SOLVENT MOLECULES HOH 776, HOH 777, HOH 778 AND HOH 779 WERE NOT INCLUDED IN REFINEMENT SINCE THEY LIE ON OR NEAR TO NON-CRYSTALLOGRAPHIC SYMMETRY AXES. SOLVENT MOLECULES WITH B > 60 A**2 WERE DELETED AFTER REFINEMENT.
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Displacement parameters | Biso mean: 20.3 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→10 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.61 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 8
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Xplor file |
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