[English] 日本語
Yorodumi- PDB-8qws: Crystal structure of CotB2 variant V80L in complex with alendronate -
+Open data
-Basic information
Entry | Database: PDB / ID: 8qws | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of CotB2 variant V80L in complex with alendronate | ||||||
Components | Cyclooctat-9-en-7-ol synthase | ||||||
Keywords | LYASE / TERPENE SYNTHASE / CYCLOOCTATIN | ||||||
Function / homology | cyclooctat-9-en-7-ol synthase / Terpene synthase family 2, C-terminal metal binding / Isoprenoid synthase domain superfamily / isomerase activity / lyase activity / metal ion binding / ACETATE ION / 4-AMINO-1-HYDROXYBUTANE-1,1-DIYLDIPHOSPHONATE / Cyclooctat-9-en-7-ol synthase Function and homology information | ||||||
Biological species | Streptomyces melanosporofaciens (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||
Authors | Dimos, N. / Himpich, S. / Ringel, M. / Driller, R. / Major, D.T. / Brueck, T. / Loll, B. | ||||||
Funding support | Germany, 1items
| ||||||
Citation | Journal: To Be Published Title: Crystal structure of CotB2 variant V80L in complex with alendronate Authors: Dimos, N. / Himpich, S. / Driller, R. / Loll, B. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 8qws.cif.gz | 179.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb8qws.ent.gz | 115 KB | Display | PDB format |
PDBx/mmJSON format | 8qws.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qw/8qws ftp://data.pdbj.org/pub/pdb/validation_reports/qw/8qws | HTTPS FTP |
---|
-Related structure data
Related structure data | 6ggjS S: Starting model for refinement |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
Unit cell |
|
-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 36784.551 Da / Num. of mol.: 2 / Mutation: V80L Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces melanosporofaciens (bacteria) Gene: CotB2 / Plasmid: pET28b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: C9K1X5 |
---|
-Non-polymers , 8 types, 347 molecules
#2: Chemical | #3: Chemical | ChemComp-MG / #4: Chemical | ChemComp-EDO / #5: Chemical | ChemComp-MPD / ( #6: Chemical | ChemComp-ACT / #7: Chemical | #8: Chemical | ChemComp-CL / | #9: Water | ChemComp-HOH / | |
---|
-Details
Has ligand of interest | Y |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 44.08 % |
---|---|
Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / Details: 7 % PEG8000, 0.15 M Mgacetate, 10% ethylenglycol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.9766 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 26, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9766 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→50 Å / Num. obs: 86123 / % possible obs: 99.9 % / Redundancy: 13.4 % / Biso Wilson estimate: 23.95 Å2 / CC1/2: 0.99 / Rrim(I) all: 0.099 / Net I/σ(I): 16.5 |
Reflection shell | Resolution: 1.6→1.7 Å / Redundancy: 13.1 % / Rmerge(I) obs: 2.54 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 13768 / CC1/2: 0.99 / % possible all: 99.8 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6GGJ Resolution: 1.6→47.16 Å / SU ML: 0.1844 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.6543 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.14 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.6→47.16 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|