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Yorodumi- PDB-6lop: Crystal Structure of Class IB terpene synthase bound with geranyl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6lop | |||||||||
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Title | Crystal Structure of Class IB terpene synthase bound with geranylgeraniol | |||||||||
Components | Tetraprenyl-beta-curcumene synthase | |||||||||
Keywords | LYASE / TERPENE SYNTHASE | |||||||||
Function / homology | Tetraprenyl-beta-curcumene synthase YtpB-like / Protein of unknown function (DUF2600) / Chem-ELX / Tetraprenyl-beta-curcumene synthase Function and homology information | |||||||||
Biological species | Bacillus alcalophilus ATCC 27647 = CGMCC 1.3604 (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.91 Å | |||||||||
Authors | Fujihashi, M. / Inagi, H. / Miki, K. | |||||||||
Funding support | Japan, 2items
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Citation | Journal: Acs Chem.Biol. / Year: 2020 Title: Characterization of Class IB Terpene Synthase: The First Crystal Structure Bound with a Substrate Surrogate. Authors: Stepanova, R. / Inagi, H. / Sugawara, K. / Asada, K. / Nishi, T. / Ueda, D. / Yasuno, Y. / Shinada, T. / Miki, K. / Fujihashi, M. / Sato, T. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6lop.cif.gz | 168 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6lop.ent.gz | 130 KB | Display | PDB format |
PDBx/mmJSON format | 6lop.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6lop_validation.pdf.gz | 763.4 KB | Display | wwPDB validaton report |
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Full document | 6lop_full_validation.pdf.gz | 766.4 KB | Display | |
Data in XML | 6lop_validation.xml.gz | 31.1 KB | Display | |
Data in CIF | 6lop_validation.cif.gz | 46 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lo/6lop ftp://data.pdbj.org/pub/pdb/validation_reports/lo/6lop | HTTPS FTP |
-Related structure data
Related structure data | 6looSC 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
#1: Protein | Mass: 41879.664 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus alcalophilus ATCC 27647 = CGMCC 1.3604 (bacteria) Gene: BALCAV_0202405 / Plasmid: pColdII / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pLysS / References: UniProt: A0A094YZ24 #2: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 2.16 Å3/Da / Density % sol: 42.94 % / Mosaicity: 0.27 ° |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion / pH: 8.3 Details: PEG3350, Ammonium Acetate, Magnesium Chloride, Methanol |
-Data collection
Diffraction | Mean temperature: 95 K / Serial crystal experiment: N | ||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å | ||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jun 28, 2018 | ||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||
Reflection | Resolution: 1.91→48.01 Å / Num. obs: 52514 / % possible obs: 96.8 % / Redundancy: 3.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.05 / Rpim(I) all: 0.031 / Rrim(I) all: 0.059 / Net I/σ(I): 10 | ||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 6LOO Resolution: 1.91→47.96 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.955 / SU B: 3.855 / SU ML: 0.109 / SU R Cruickshank DPI: 0.1619 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.162 / ESU R Free: 0.142 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: 92.15 Å2 / Biso mean: 32.861 Å2 / Biso min: 17.89 Å2
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Refinement step | Cycle: final / Resolution: 1.91→47.96 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.91→1.96 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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