[English] 日本語
Yorodumi- PDB-6sbd: Structure of type II terpene cyclase MstE_D109A from Scytonema in... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6sbd | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Structure of type II terpene cyclase MstE_D109A from Scytonema in complex with merosterolic acid A (product) | |||||||||
Components | MstE | |||||||||
Keywords | BIOSYNTHETIC PROTEIN / Type II Terpene Cyclase / Marine Drugs / Merosterol / Alpha6-Alpha6 Barrel | |||||||||
Function / homology | Squalene cyclase, C-terminal / Squalene-hopene cyclase C-terminal domain / Terpenoid cyclases/protein prenyltransferase alpha-alpha toroid / Chem-L4B / MstE Function and homology information | |||||||||
Biological species | Scytonema sp. PCC 10023 (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å | |||||||||
Authors | Moosmann, P. / Ecker, F. / Leopold-Messer, S. / Cahn, J.K.B. / Groll, M. / Piel, J. | |||||||||
Funding support | Switzerland, 2items
| |||||||||
Citation | Journal: Nat.Chem. / Year: 2020 Title: A monodomain class II terpene cyclase assembles complex isoprenoid scaffolds. Authors: Moosmann, P. / Ecker, F. / Leopold-Messer, S. / Cahn, J.K.B. / Dieterich, C.L. / Groll, M. / Piel, J. | |||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6sbd.cif.gz | 168 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6sbd.ent.gz | 130.7 KB | Display | PDB format |
PDBx/mmJSON format | 6sbd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6sbd_validation.pdf.gz | 817.9 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 6sbd_full_validation.pdf.gz | 818.6 KB | Display | |
Data in XML | 6sbd_validation.xml.gz | 18 KB | Display | |
Data in CIF | 6sbd_validation.cif.gz | 27.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sb/6sbd ftp://data.pdbj.org/pub/pdb/validation_reports/sb/6sbd | HTTPS FTP |
-Related structure data
Related structure data | 6sbbSC 6sbcC 6sbeC 6sbfC 6sbgC S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 40608.395 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Scytonema sp. PCC 10023 (bacteria) / Gene: mstE / Production host: Escherichia coli (E. coli) / References: UniProt: A0A2D1CM82 | ||||||||
---|---|---|---|---|---|---|---|---|---|
#2: Chemical | ChemComp-GOL / #3: Chemical | ChemComp-MPD / ( | #4: Chemical | ChemComp-L4B / ( | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.07 Å3/Da / Density % sol: 40.56 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 100 mM HEPES, 1 M LiCl, 30% PEG 6000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 1, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→50 Å / Num. obs: 66812 / % possible obs: 99.4 % / Redundancy: 5.1 % / Rmerge(I) obs: 0.053 / Net I/σ(I): 16 |
Reflection shell | Resolution: 1.4→1.5 Å / Rmerge(I) obs: 0.501 / Mean I/σ(I) obs: 3.5 / Num. unique obs: 12352 / % possible all: 99.3 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6SBB Resolution: 1.4→15 Å / Cor.coef. Fo:Fc: 0.985 / Cor.coef. Fo:Fc free: 0.977 / SU B: 1.775 / SU ML: 0.031 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.047 / ESU R Free: 0.047 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 167.49 Å2 / Biso mean: 16.437 Å2 / Biso min: 8.47 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.4→15 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.4→1.436 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
|