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Yorodumi- PDB-1iwp: Glycerol Dehydratase-cyanocobalamin Complex of Klebsiella pneumoniae -
+Open data
-Basic information
Entry | Database: PDB / ID: 1iwp | ||||||
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Title | Glycerol Dehydratase-cyanocobalamin Complex of Klebsiella pneumoniae | ||||||
Components | (Glycerol Dehydratase ...) x 3 | ||||||
Keywords | LYASE / B12 / GLYCEROL DEHYDRATASE / KLEBSIELLA PNEUMONIAE / COBALAMIN / RADICAL CATALYSIS | ||||||
Function / homology | Function and homology information glycerol dehydratase / glycerol dehydratase activity / propanediol dehydratase / propanediol dehydratase activity / cobalamin binding Similarity search - Function | ||||||
Biological species | Klebsiella pneumoniae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Yamanishi, M. / Yunoki, M. / Tobimatsu, T. / Toraya, T. | ||||||
Citation | Journal: Eur.J.Biochem. / Year: 2002 Title: The crystal structure of coenzyme B12-dependent glycerol dehydratase in complex with cobalamin and propane-1,2-diol. Authors: Yamanishi, M. / Yunoki, M. / Tobimatsu, T. / Sato, H. / Matsui, J. / Dokiya, A. / Iuchi, Y. / Oe, K. / Suto, K. / Shibata, N. / 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 | 1iwp.cif.gz | 371.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1iwp.ent.gz | 295.4 KB | Display | PDB format |
PDBx/mmJSON format | 1iwp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1iwp_validation.pdf.gz | 575.4 KB | Display | wwPDB validaton report |
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Full document | 1iwp_full_validation.pdf.gz | 647.1 KB | Display | |
Data in XML | 1iwp_validation.xml.gz | 45.9 KB | Display | |
Data in CIF | 1iwp_validation.cif.gz | 69.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/iw/1iwp ftp://data.pdbj.org/pub/pdb/validation_reports/iw/1iwp | HTTPS FTP |
-Related structure data
Related structure data | 1dioS S: Starting model for refinement |
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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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-Components
-Glycerol Dehydratase ... , 3 types, 6 molecules ALBEGM
#1: Protein | Mass: 60714.555 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Strain: ATCC 25955 / Plasmid: pUSI2E / Production host: Escherichia coli (E. coli) / References: UniProt: Q59476, glycerol dehydratase #2: Protein | Mass: 21385.490 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Strain: ATCC 25955 / Plasmid: pUSI2E, pET19b / Production host: Escherichia coli (E. coli) / References: UniProt: O08505, glycerol dehydratase #3: Protein | Mass: 16128.362 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Strain: ATCC 25955 / Plasmid: pUSI2E / Production host: Escherichia coli (E. coli) / References: UniProt: Q59475, glycerol dehydratase |
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-Non-polymers , 4 types, 887 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: 3.03 Å3/Da / Density % sol: 51 % | ||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion (sandwitch drop) / pH: 8 Details: 20mM Tris-HCl, 15% PEG6000, 0.2M Na2SO4, pH 8.0, VAPOR DIFFUSION (Sandwitch Drop), temperature 277K | ||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / Method: sandwich-drop vapor diffusion / Details: Shibata, N., (1999) Structure, 7, 997. | ||||||||||||||||||||
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: BL40B2 / Wavelength: 0.816 Å |
Detector | Type: ADSC QUANTUM 4r / Detector: CCD / Date: Jan 19, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.816 Å / Relative weight: 1 |
Reflection | Resolution: 2→45.175 Å / Num. all: 130797 / Num. obs: 130797 / % possible obs: 99.6 % / Observed criterion σ(I): 3 / Redundancy: 3.6 % / Rmerge(I) obs: 0.087 / Rsym value: 0.132 / Net I/σ(I): 4.8 |
Reflection shell | Resolution: 2→2.11 Å / Redundancy: 3 % / % possible all: 97.6 |
Reflection | *PLUS Num. obs: 130635 / Num. measured all: 958394 / Rmerge(I) obs: 0.097 |
Reflection shell | *PLUS % possible obs: 97.6 % / Rmerge(I) obs: 0.38 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB id, 1DIO Resolution: 2.1→45 Å / σ(F): 0
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Displacement parameters | Biso mean: 28.73 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.1→45 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.18 Å / Total num. of bins used: 10
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Refinement | *PLUS Lowest resolution: 45 Å / % reflection Rfree: 10 % / Rfactor Rfree: 0.248 / Rfactor Rwork: 0.208 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.3036 / Rfactor Rwork: 0.2606 |