+Open data
-Basic information
Entry | Database: PDB / ID: 3auj | ||||||
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Title | Structure of diol dehydratase complexed with glycerol | ||||||
Components | (Diol dehydrase ...) x 3 | ||||||
Keywords | LYASE / ALPHA/BETA 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 / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Yamanishi, M. / Kinoshita, K. / Fukuoka, M. / Shibata, T. / Tobimatsu, T. / Toraya, T. | ||||||
Citation | Journal: Febs J. / Year: 2012 Title: Redesign of coenzyme B(12) dependent diol dehydratase to be resistant to the mechanism-based inactivation by glycerol and act on longer chain 1,2-diols Authors: Yamanishi, M. / Kinoshita, K. / Fukuoka, M. / Saito, T. / Tanokuchi, A. / Ikeda, Y. / Obayashi, H. / Mori, K. / Shibata, N. / Tobimatsu, T. / Toraya, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3auj.cif.gz | 382.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3auj.ent.gz | 302.7 KB | Display | PDB format |
PDBx/mmJSON format | 3auj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/au/3auj ftp://data.pdbj.org/pub/pdb/validation_reports/au/3auj | HTTPS FTP |
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-Related structure data
Related structure data | 1egmS 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 on special symmetry positions |
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-Components
-Diol dehydrase ... , 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) / Gene: pddA / Plasmid: PUSI2E / 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) / Gene: pddB / Plasmid: PUSI2E / 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) / Gene: pddC / Plasmid: PUSI2E / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q59472, propanediol dehydratase |
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-Non-polymers , 5 types, 1383 molecules
#4: Chemical | #5: Chemical | #6: Chemical | ChemComp-PO4 / #7: Chemical | #8: 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: 3.49 Å3/Da / Density % sol: 64.74 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion / pH: 8 Details: 14-18%(W/V) PEG 6000, 0.23-0.25M AMMONIUM SULFATE, 0.02M TRIS-HCL, 0.2%(W/V) LDAO, pH 8.0, VAPOR DIFFUSION, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Nov 9, 2001 / Details: MIRRORS |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→50 Å / Num. all: 157499 / Num. obs: 157499 / % possible obs: 95.6 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 3.4 % / Biso Wilson estimate: 11.3 Å2 / Rmerge(I) obs: 0.064 / Net I/σ(I): 16.45 |
Reflection shell | Resolution: 2.1→2.14 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 2.99 / % possible all: 84.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1EGM Resolution: 2.1→40.34 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 253513.72 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 58.6715 Å2 / ksol: 0.35 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.1→40.34 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.14 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 20
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Xplor file |
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