+Open data
-Basic information
Entry | Database: PDB / ID: 5g1w | |||||||||
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Title | Apo Structure of Linalool Dehydratase-Isomerase | |||||||||
Components | LINALOOL DEHYDRATASE/ISOMERASE | |||||||||
Keywords | LYASE / HYDRATASE / ISOMERASE / TERPENE / ALKENE | |||||||||
Function / homology | Function and homology information linalool dehydratase / geraniol isomerase / monoterpene catabolic process / intramolecular hydroxytransferase activity / monoterpenoid metabolic process / hydro-lyase activity / cellular response to organic substance / protein tetramerization / periplasmic space Similarity search - Function | |||||||||
Biological species | CASTELLANIELLA DEFRAGRANS (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.76 Å | |||||||||
Authors | Chambers, S. / Hau, A. / Man, H. / Omar, M. / Turkenburg, J.P. / Grogan, G. | |||||||||
Citation | Journal: Nat. Chem. Biol. / Year: 2017 Title: Structural and functional insights into asymmetric enzymatic dehydration of alkenols. Authors: Nestl, B.M. / Geinitz, C. / Popa, S. / Rizek, S. / Haselbeck, R.J. / Stephen, R. / Noble, M.A. / Fischer, M.P. / Ralph, E.C. / Hau, H.T. / Man, H. / Omar, M. / Turkenburg, J.P. / van Dien, S. ...Authors: Nestl, B.M. / Geinitz, C. / Popa, S. / Rizek, S. / Haselbeck, R.J. / Stephen, R. / Noble, M.A. / Fischer, M.P. / Ralph, E.C. / Hau, H.T. / Man, H. / Omar, M. / Turkenburg, J.P. / van Dien, S. / Culler, S.J. / Grogan, G. / Hauer, B. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5g1w.cif.gz | 400.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5g1w.ent.gz | 331.8 KB | Display | PDB format |
PDBx/mmJSON format | 5g1w.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g1/5g1w ftp://data.pdbj.org/pub/pdb/validation_reports/g1/5g1w | 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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Components on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
#1: Protein | Mass: 41993.715 Da / Num. of mol.: 5 Source method: isolated from a genetically manipulated source Source: (gene. exp.) CASTELLANIELLA DEFRAGRANS (bacteria) / Strain: 65PHEN / Plasmid: PET-YSBLIC-3C / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) References: UniProt: E1XUJ2, linalool dehydratase, geraniol isomerase #2: Chemical | ChemComp-EDO / #3: Chemical | #4: 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: 2.77 Å3/Da / Density % sol: 55.6 % / Description: NONE |
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Crystal grow | pH: 6.5 Details: 0.1 M BIS-TRIS PROPANE BUFFER PH 6.5 WITH 25% (W/V) PEG 3350, 10% (W/V) METHYLPENTANE DIOL AND 0.1 M SODIUM MALONATE |
-Data collection
Diffraction | Mean temperature: 120 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97949 |
Detector | Date: Apr 19, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97949 Å / Relative weight: 1 |
Reflection | Resolution: 1.76→47.97 Å / Num. obs: 218882 / % possible obs: 97 % / Observed criterion σ(I): 2 / Redundancy: 4.2 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 10.6 |
Reflection shell | Resolution: 1.76→1.79 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.67 / Mean I/σ(I) obs: 1.7 / % possible all: 95.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: SEMET STRUCTURE Resolution: 1.76→47.97 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.959 / SU B: 2.242 / SU ML: 0.067 / Cross valid method: THROUGHOUT / ESU R: 0.093 / ESU R Free: 0.09 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.75 Å2
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Refinement step | Cycle: LAST / Resolution: 1.76→47.97 Å
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Refine LS restraints |
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