+Open data
-Basic information
Entry | Database: PDB / ID: 1iwb | ||||||
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Title | Crystal structure of diol dehydratase | ||||||
Components | (DIOL DEHYDRATASE ...) x 3 | ||||||
Keywords | LYASE / beta-alpha-barrels | ||||||
Function / homology | Function and homology information propanediol dehydratase / propanediol dehydratase activity / cobalamin binding / metal ion binding Similarity search - Function | ||||||
Biological species | Klebsiella oxytoca (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å | ||||||
Authors | Shibata, N. / Masuda, J. / Morimoto, Y. / Yasuoka, N. / Toraya, T. | ||||||
Citation | Journal: Biochemistry / Year: 2002 Title: Substrate-induced conformational change of a coenzyme B12-dependent enzyme: crystal structure of the substrate-free form of diol dehydratase Authors: Shibata, N. / Masuda, J. / Morimoto, Y. / Yasuoka, N. / Toraya, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1iwb.cif.gz | 366.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1iwb.ent.gz | 296.8 KB | Display | PDB format |
PDBx/mmJSON format | 1iwb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/iw/1iwb ftp://data.pdbj.org/pub/pdb/validation_reports/iw/1iwb | HTTPS FTP |
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-Related structure data
Related structure data | |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
-DIOL DEHYDRATASE ... , 3 types, 6 molecules ALBEGM
#1: Protein | Mass: 60408.133 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Klebsiella oxytoca (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: Q59470, propanediol dehydratase #2: Protein | Mass: 24141.678 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Klebsiella oxytoca (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: Q59471, propanediol dehydratase #3: Protein | Mass: 19198.695 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Klebsiella oxytoca (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: Q59472, propanediol dehydratase |
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-Non-polymers , 3 types, 970 molecules
#4: Chemical | ChemComp-K / #5: Chemical | #6: 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: 2.32 Å3/Da / Density % sol: 46.96 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 278 K / Method: vapor diffusion / pH: 8 Details: PEG6000, potassium phosphate, Tris, lithium chloride, N,N-dimethyllaurylamineoxide, pH 8.0, VAPOR DIFFUSION, temperature 278K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / Method: sandwich-drop vapor diffusion | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.708 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Apr 14, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.708 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→50 Å / Num. all: 1656266 / Num. obs: 126694 / % possible obs: 76.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
Reflection shell | Resolution: 1.85→1.92 Å / % possible all: 53.6 |
Reflection | *PLUS Lowest resolution: 50 Å / Num. measured all: 1656266 / Rmerge(I) obs: 0.054 |
Reflection shell | *PLUS % possible obs: 53.6 % / Rmerge(I) obs: 0.176 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.85→10 Å / σ(F): 1 / σ(I): 1 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 1.85→10 Å
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Refine LS restraints |
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Software | *PLUS Name: SHELXL / Version: 97 / Classification: refinement | ||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS |