+Open data
-Basic information
Entry | Database: PDB / ID: 1a0d | ||||||
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Title | XYLOSE ISOMERASE FROM BACILLUS STEAROTHERMOPHILUS | ||||||
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 | Geobacillus stearothermophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3 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: Biotechnol.Lett. / Year: 1993 Title: High Level Expression of a Thermostable Bacillus Xylose (Glucose) Isomerase in Escherichia Coli Authors: Wuxiang, L. / Jeyaseelan, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1a0d.cif.gz | 343.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1a0d.ent.gz | 285.3 KB | Display | PDB format |
PDBx/mmJSON format | 1a0d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1a0d_validation.pdf.gz | 450.6 KB | Display | wwPDB validaton report |
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Full document | 1a0d_full_validation.pdf.gz | 487.9 KB | Display | |
Data in XML | 1a0d_validation.xml.gz | 63 KB | Display | |
Data in CIF | 1a0d_validation.cif.gz | 86.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a0/1a0d ftp://data.pdbj.org/pub/pdb/validation_reports/a0/1a0d | HTTPS FTP |
-Related structure data
Related structure data | 1a0cC 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: 50073.395 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Geobacillus stearothermophilus (bacteria) / Cellular location: CYTOPLASM / Strain: LLD-R / References: UniProt: P54273, xylose isomerase #2: Chemical | ChemComp-MN / #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: 2.7 Å3/Da / Density % sol: 45 % |
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 6.5 Details: VAPOR DIFFUSION FROM HANGING DROPS (18 DEG C): PROTEIN (A280 22) WAS IN 50 MM TRIS, 10 MM MNCL2, PH 7.5; RESERVOIR SOLUTION WAS 10% PEG, 100 MM LICL, 100 MM MES, PH 6.3; DROPS WERE FORMED ...Details: VAPOR DIFFUSION FROM HANGING DROPS (18 DEG C): PROTEIN (A280 22) WAS IN 50 MM TRIS, 10 MM MNCL2, PH 7.5; RESERVOIR SOLUTION WAS 10% PEG, 100 MM LICL, 100 MM MES, PH 6.3; DROPS WERE FORMED FROM EQUAL PARTS OF PROTEIN AND RESERVOIR SOLUTIONS., pH 6.5, vapor diffusion - hanging drop PH range: 6.3 - 7.5 |
-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: ROTATING ANODE / Type: ELLIOTT GX-21 / Wavelength: 1.5418 |
Detector | Type: ENRAF-NONIUS FAST / Detector: DIFFRACTOMETER / Date: Feb 1, 1993 / Details: DUAL SLITS, COLLIMATOR |
Radiation | Monochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 3→33 Å / Num. obs: 35985 / % possible obs: 89.6 % / Redundancy: 1.7 % / Biso Wilson estimate: 49.8 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 7.1 |
Reflection shell | Resolution: 3→3.16 Å / Redundancy: 1.5 % / Rmerge(I) obs: 0.23 / Mean I/σ(I) obs: 3.1 / % possible all: 62.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 6XIA Resolution: 3→20 Å / Rfactor Rfree error: 0.005 / Cross valid method: A POSTERIORI Details: OCCUPANCIES OF THE MN CATIONS AND WATER HOH 501 WERE REFINED, SIMULTANEOUSLY WITH TEMPERATURE FACTORS FOR ALL ATOMS, USING THE GROUP B COMMAND IN X-PLOR. THESE OCCUPANCIES WERE THEN FIXED AT ...Details: OCCUPANCIES OF THE MN CATIONS AND WATER HOH 501 WERE REFINED, SIMULTANEOUSLY WITH TEMPERATURE FACTORS FOR ALL ATOMS, USING THE GROUP B COMMAND IN X-PLOR. THESE OCCUPANCIES WERE THEN FIXED AT ROUNDED VALUES FOR THE SUBSEQUENT REFINEMENT PROTOCOL. DISORDERED SIDE CHAINS WERE NOT INCLUDED IN REFINEMENT.
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Displacement parameters | Biso mean: 19.1 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3→3.14 Å / Rfactor Rfree error: 0.025 / Total num. of bins used: 8
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Xplor file |
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