+Open data
-Basic information
Entry | Database: PDB / ID: 1mmf | ||||||
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Title | Crystal structure of substrate free form of glycerol dehydratase | ||||||
Components | (glycerol dehydrase ...) x 3 | ||||||
Keywords | LYASE / Glycerol dehydratase / Diol dehydratase / Coenzyme B12 / TIM barrel | ||||||
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: 2.5 Å | ||||||
Authors | Liao, D.I. / Dotson, G. / Turner, I. / Reiss, L. / Emptage, M. | ||||||
Citation | Journal: J.Inorg.Biochem. / Year: 2003 Title: Crystal structure of substrate free form of glycerol dehydratase Authors: Liao, D.I. / Dotson, G. / Turner, I. / Reiss, L. / Emptage, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1mmf.cif.gz | 345.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1mmf.ent.gz | 277.5 KB | Display | PDB format |
PDBx/mmJSON format | 1mmf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1mmf_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 1mmf_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 1mmf_validation.xml.gz | 71.5 KB | Display | |
Data in CIF | 1mmf_validation.cif.gz | 95.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mm/1mmf ftp://data.pdbj.org/pub/pdb/validation_reports/mm/1mmf | 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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2 |
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3 |
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Unit cell |
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Details | The biologyical assembly of glycerol dehydratase is a heterohexamer. It is a dimer of alpha-beta-gamma trimers. The asymmetric unit in the crystal contains an entire heterohexamer. Chain names for subunits are A, B, and G fare one trimer and L, E and M for the second trimer. |
-Components
-Glycerol dehydrase ... , 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) / Plasmid: pBluescript SKII / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21DE3 / References: UniProt: Q59476, glycerol dehydratase #2: Protein | Mass: 21353.424 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Plasmid: pBluescript SKII / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21DE3 / 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) / Plasmid: pBluescript SKII / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21DE3 / References: UniProt: Q59475, glycerol dehydratase |
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-Non-polymers , 3 types, 211 molecules
#4: Chemical | #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: 2.87 Å3/Da / Density % sol: 57.12 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 9.4 Details: Amonium sulfate, RbCl2, CdCl2, cyanocobalamin, CHES, pH 9.4, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7.5 / Method: vapor diffusion, hanging 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: APS / Beamline: 5ID-B / Wavelength: 1 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Aug 11, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→30 Å / Num. all: 67426 / Num. obs: 67426 / % possible obs: 87.7 % / Observed criterion σ(I): -3 / Rmerge(I) obs: 0.072 / Net I/σ(I): 11.6 |
Reflection shell | Resolution: 2.5→2.54 Å / Rmerge(I) obs: 0.14 / Mean I/σ(I) obs: 3.1 / % possible all: 50.1 |
Reflection | *PLUS Lowest resolution: 30 Å / Num. measured all: 302300 |
Reflection shell | *PLUS Highest resolution: 2.5 Å / % possible obs: 50.1 % / Rmerge(I) obs: 0.14 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1DIO Resolution: 2.5→30 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.5→30 Å
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Refine LS restraints |
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Refinement | *PLUS % reflection Rfree: 5 % | |||||||||||||||
Solvent computation | *PLUS | |||||||||||||||
Displacement parameters | *PLUS |