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Yorodumi- PDB-1egm: CRYSTAL STRUCTURE OF DIOL DEHYDRATASE-CYANOCOBALAMIN COMPLEX AT 100K. -
+Open data
-Basic information
Entry | Database: PDB / ID: 1egm | |||||||||
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Title | CRYSTAL STRUCTURE OF DIOL DEHYDRATASE-CYANOCOBALAMIN COMPLEX AT 100K. | |||||||||
Components | (PROPANEDIOL DEHYDRATASE) x 3 | |||||||||
Keywords | LYASE / CYANOCOBALAMIN / 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: 1.85 Å | |||||||||
Authors | Masuda, J. / Shibata, N. / 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 | 1egm.cif.gz | 378.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1egm.ent.gz | 301.8 KB | Display | PDB format |
PDBx/mmJSON format | 1egm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1egm_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 1egm_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 1egm_validation.xml.gz | 79.3 KB | Display | |
Data in CIF | 1egm_validation.cif.gz | 114.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/eg/1egm ftp://data.pdbj.org/pub/pdb/validation_reports/eg/1egm | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | The biological assembly is heterohexamer constructed from A, B, G, L, E, G chains and two cyanocobalamins. |
-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, 1217 molecules
#4: Chemical | #5: Chemical | #6: Chemical | #7: 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: 2.25 Å3/Da / Density % sol: 45.35 % | |||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sandwich / pH: 8 Details: PEG6000, potassium phosphate, Tris, lauryldimethylamine oxide, ammonium sulfate, propane diol, cyanocobalamin, pH 8.0, VAPOR DIFFUSION, SANDWICH, temperature 277K | |||||||||||||||||||||||||
Crystal grow | *PLUS Details: Masuda, J., (1999) Acta Crystallogr, D55, 907. / Method: vapor diffusion, sandwich drop | |||||||||||||||||||||||||
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: 1 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Oct 3, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→40 Å / Num. all: 142052 / Num. obs: 142006 / % possible obs: 88.6 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 5.4 % / Biso Wilson estimate: 19.8 Å2 / Rmerge(I) obs: 0.072 / Net I/σ(I): 21.9 |
Reflection shell | Resolution: 1.85→1.88 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.134 / Num. unique all: 5330 / % possible all: 67.7 |
Reflection | *PLUS Num. obs: 142053 / Num. measured all: 1939544 |
Reflection shell | *PLUS % possible obs: 67.7 % |
-Processing
Software |
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Refinement | Resolution: 1.85→30 Å / σ(F): 1 / σ(I): 1 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 1.85→30 Å
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Refine LS restraints |
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Software | *PLUS Name: SHELXL-97 / Classification: refinement | ||||||||||||||||||||
Refinement | *PLUS Rfactor Rfree: 0.243 / Rfactor Rwork: 0.182 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS |