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Yorodumi- PDB-1eex: CRYSTAL STRUCTURE OF THE DIOL DEHYDRATASE-ADENINYLPENTYLCOBALAMIN... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1eex | ||||||
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Title | CRYSTAL STRUCTURE OF THE DIOL DEHYDRATASE-ADENINYLPENTYLCOBALAMIN COMPLEX FROM KLEBSIELLA OXYTOCA | ||||||
Components | (PROPANEDIOL DEHYDRATASE) x 3 | ||||||
Keywords | LYASE / COENZYME B12 / PROPANEDIOL / POTASSIUM ION / TIM BARREL | ||||||
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 / Resolution: 1.7 Å | ||||||
Authors | Shibata, N. / Masuda, J. / Toraya, T. / Morimoto, Y. / Yasuoka, N. | ||||||
Citation | Journal: Structure Fold.Des. / Year: 2000 Title: How a protein generates a catalytic radical from coenzyme B(12): X-ray structure of a diol-dehydratase-adeninylpentylcobalamin complex. Authors: Masuda, J. / Shibata, N. / Morimoto, Y. / Toraya, T. / Yasuoka, N. #1: Journal: Structure / Year: 1999 Title: A new mode of B12 binding and the direct participation of a potassium ion in enzyme catalysis: X-ray structure of diol dehydratase Authors: Shibata, N. / Masuda, J. / Toraya, T. / Morimoto, Y. / Yasuoka, N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1eex.cif.gz | 401.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1eex.ent.gz | 316.5 KB | Display | PDB format |
PDBx/mmJSON format | 1eex.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ee/1eex ftp://data.pdbj.org/pub/pdb/validation_reports/ee/1eex | 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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Details | The protein exists as a dimer of heterotrimers. |
-Components
-Protein , 3 types, 6 molecules ALBEGM
#1: Protein | Mass: 60408.133 Da / Num. of mol.: 2 / Fragment: ALPHA CHAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) Klebsiella oxytoca (bacteria) / Plasmid: PUC119 / Production host: Escherichia coli (E. coli) / References: UniProt: Q59470, propanediol dehydratase #2: Protein | Mass: 24141.678 Da / Num. of mol.: 2 / Fragment: BETA CHAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) Klebsiella oxytoca (bacteria) / Plasmid: PUC119 / Production host: Escherichia coli (E. coli) / References: UniProt: Q59471, propanediol dehydratase #3: Protein | Mass: 19198.695 Da / Num. of mol.: 2 / Fragment: GAMMA CHAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) Klebsiella oxytoca (bacteria) / Plasmid: PUC119 / Production host: Escherichia coli (E. coli) / References: UniProt: Q59472, propanediol dehydratase |
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-Non-polymers , 4 types, 1880 molecules
#4: Chemical | ChemComp-K / #5: Chemical | #6: Chemical | #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 2.23 Å3/Da / Density % sol: 44.77 % | |||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sandwich drop / pH: 8 Details: PEG 6000, potassium phospate, Tris-HCl, LDAO, ammonium sulfate, propane diol, adeninylpentylcobalamin,, pH 8.0, vapor diffusion, sandwich drop, temperature 277K | |||||||||||||||||||||||||
Crystal grow | *PLUS Details: Masuda, J., (1999) Acta Crystallogr, D55, 907. | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction |
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Diffraction source |
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Detector |
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Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength | Wavelength: 0.7 Å / Relative weight: 1 | |||||||||||||||
Reflection | Resolution: 1.7→100 Å / Num. all: 206373 / Num. obs: 177514 / % possible obs: 86 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 9.49 % / Biso Wilson estimate: 14.1 Å2 / Rmerge(I) obs: 0.079 / Net I/σ(I): 17.8 | |||||||||||||||
Reflection shell | Resolution: 1.7→1.76 Å / Redundancy: 4.83 % / Rmerge(I) obs: 0.171 / Num. unique all: 12631 / % possible all: 61.8 | |||||||||||||||
Reflection | *PLUS Num. measured all: 4543847 | |||||||||||||||
Reflection shell | *PLUS % possible obs: 61.8 % |
-Processing
Software |
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Refinement | Resolution: 1.7→30 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 1.7→30 Å
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Refine LS restraints |
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Software | *PLUS Name: SHELXL-97 / Classification: refinement | ||||||||||||||||||||
Refinement | *PLUS Highest resolution: 1.7 Å / Lowest resolution: 30 Å / σ(F): 0 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS |