+Open data
-Basic information
Entry | Database: PDB / ID: 6m5n | ||||||
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Title | Apo-Form Structure of Borneol Dehydrogenase | ||||||
Components | Borneol dehydrogenase | ||||||
Keywords | OXIDOREDUCTASE / terpenoid / alcohol | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Pseudomonas sp. TCU-HL1 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.84 Å | ||||||
Authors | Khine, A.A. / Huang, K.F. / Ko, T.P. / Chen, H.P. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.F / Year: 2020 Title: Structural characterization of borneol dehydrogenase from Pseudomonas sp. TCU-HL1 Authors: Khine, A.A. / Huang, K.F. / Ko, T.P. / Chen, H.P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6m5n.cif.gz | 83.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6m5n.ent.gz | 49.4 KB | Display | PDB format |
PDBx/mmJSON format | 6m5n.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m5/6m5n ftp://data.pdbj.org/pub/pdb/validation_reports/m5/6m5n | HTTPS FTP |
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-Related structure data
Related structure data | 3ak4S S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 27635.451 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas sp. TCU-HL1 (bacteria) / Gene: THL1_4180 / Plasmid: pET-30a / Production host: Escherichia Coli BL21(DE3) (bacteria) / References: UniProt: A0A1B3EB36 | ||||
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#2: Chemical | ChemComp-SO4 / | ||||
#3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.23 Å3/Da / Density % sol: 44.81 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.5 / Details: PEG 8000, sodium acetate, lithium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: BL15A1 / Wavelength: 1 Å |
Detector | Type: RAYONIX MX300HE / Detector: CCD / Date: Nov 7, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.84→30 Å / Num. obs: 21642 / % possible obs: 100 % / Redundancy: 5 % / Biso Wilson estimate: 20.51 Å2 / CC1/2: 0.918 / Rmerge(I) obs: 0.137 / Rpim(I) all: 0.067 / Net I/σ(I): 11.54 |
Reflection shell | Resolution: 1.84→1.91 Å / Redundancy: 5 % / Rmerge(I) obs: 0.842 / Mean I/σ(I) obs: 2.03 / Num. unique obs: 2120 / CC1/2: 0.679 / Rpim(I) all: 0.413 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB 3ak4 Resolution: 1.84→25.55 Å / SU ML: 0.1878 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 17.2282
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.62 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.84→25.55 Å
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Refine LS restraints |
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LS refinement shell |
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