+Open data
-Basic information
Entry | Database: PDB / ID: 6thm | ||||||
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Title | Linalool Dehydratase Isomerase M125A mutant | ||||||
Components | Linalool dehydratase-isomerase protein LDI | ||||||
Keywords | LYASE / Alkene / Alkenol / Hydratase | ||||||
Function / homology | Function and homology information linalool dehydratase / geraniol isomerase / monoterpene catabolic process / intramolecular hydroxytransferase activity / monoterpenoid metabolic process / hydro-lyase activity / : / protein tetramerization / periplasmic space Similarity search - Function | ||||||
Biological species | Castellaniella defragrans 65Phen (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.99 Å | ||||||
Authors | Cuetos, A. / Zukic, E. / Danesh-Azari, H.R. / Grogan, G. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: Acs Catalysis / Year: 2020 Title: Mutational Analysis of Linalool Dehydratase Isomerase Suggests That Alcohol and Alkene Transformations Are Catalyzed Using Noncovalent Mechanisms Authors: Cuetos, A. / Iglesias-Fernandez, J. / Danesh-Azari, H.R. / Zukic, E. / Dowle, A. / Osuna, S. / Grogan, G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6thm.cif.gz | 374.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6thm.ent.gz | 306.3 KB | Display | PDB format |
PDBx/mmJSON format | 6thm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6thm_validation.pdf.gz | 476.7 KB | Display | wwPDB validaton report |
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Full document | 6thm_full_validation.pdf.gz | 487.6 KB | Display | |
Data in XML | 6thm_validation.xml.gz | 69.5 KB | Display | |
Data in CIF | 6thm_validation.cif.gz | 99.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/th/6thm ftp://data.pdbj.org/pub/pdb/validation_reports/th/6thm | HTTPS FTP |
-Related structure data
Related structure data | 6t9hC 6tfnC 6tfrC 6tftC 5g1uS S: Starting model for refinement C: citing same article (ref.) |
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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
#1: Protein | Mass: 41933.598 Da / Num. of mol.: 5 Source method: isolated from a genetically manipulated source Details: M125A mutant Source: (gene. exp.) Castellaniella defragrans 65Phen (bacteria) Gene: BN940_14136 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: W8X534 #2: Chemical | ChemComp-EDO / #3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
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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: 2.82 Å3/Da / Density % sol: 56.39 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.2 M sodium malonate; 0.1 M bis-tris propane pH 7.5; 20% (w/w) PEG3350; 5% (v/v) methylpentanediol |
-Data collection
Diffraction | Mean temperature: 120 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 20, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97625 Å / Relative weight: 1 |
Reflection | Resolution: 1.99→98.33 Å / Num. obs: 156439 / % possible obs: 98.4 % / Redundancy: 4.2 % / CC1/2: 1 / Rmerge(I) obs: 0.08 / Rpim(I) all: 0.07 / Net I/σ(I): 9.1 |
Reflection shell | Resolution: 1.99→2.02 Å / Rmerge(I) obs: 0.91 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 7677 / CC1/2: 0.68 / Rpim(I) all: 0.77 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5G1U Resolution: 1.99→96.18 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.947 / SU B: 4.662 / SU ML: 0.122 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.152 / ESU R Free: 0.141 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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 max: 95.42 Å2 / Biso mean: 33.191 Å2 / Biso min: 21.02 Å2
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Refinement step | Cycle: final / Resolution: 1.99→96.18 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.99→2.042 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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