+Open data
-Basic information
Entry | Database: PDB / ID: 8sk0 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal structure of EvdS6 decarboxylase in ligand bound state | |||||||||
Components | dTDP-glucose 4,6-dehydratase | |||||||||
Keywords | LYASE / Decarboxylase / NDP- glucuronic acid / TDP / citrate | |||||||||
Function / homology | Function and homology information dTDP-glucose 4,6-dehydratase / dTDP-glucose 4,6-dehydratase activity / nucleotide-sugar metabolic process Similarity search - Function | |||||||||
Biological species | Micromonospora carbonacea (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.51 Å | |||||||||
Authors | Sharma, P. / Frigo, L. / Dulin, C.C. / Bachmann, B.O. / Iverson, T.M. | |||||||||
Funding support | United States, 2items
| |||||||||
Citation | Journal: J.Biol.Chem. / Year: 2023 Title: EvdS6 is a bifunctional decarboxylase from the everninomicin gene cluster. Authors: Dulin, C.C. / Sharma, P. / Frigo, L. / Voehler, M.W. / Iverson, T.M. / Bachmann, B.O. | |||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 8sk0.cif.gz | 194.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb8sk0.ent.gz | 125 KB | Display | PDB format |
PDBx/mmJSON format | 8sk0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sk/8sk0 ftp://data.pdbj.org/pub/pdb/validation_reports/sk/8sk0 | HTTPS FTP |
---|
-Related structure data
Related structure data | 8shhC C: citing same article (ref.) |
---|---|
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: 37770.359 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Micromonospora carbonacea (bacteria) / Gene: GA0070563_112236 / Production host: Escherichia coli (E. coli) References: UniProt: A0A1C5ADV9, dTDP-glucose 4,6-dehydratase |
---|
-Non-polymers , 6 types, 837 molecules
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-TYD / | #5: Chemical | ChemComp-PEG / | #6: Chemical | ChemComp-FLC / | #7: 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: 2.25 Å3/Da / Density % sol: 45.41 % |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop Details: Protein concentration= 9mg/ml, Reservoir solution= 2% v/v tacsimate pH 5.0, 100mM sodium citrate tribasic dihydrate pH 5.6, 16% w/v polyethylene glycol [PEG] 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97857 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 21, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97857 Å / Relative weight: 1 |
Reflection | Resolution: 1.51→50 Å / Num. obs: 106406 / % possible obs: 98.9 % / Redundancy: 4 % / Biso Wilson estimate: 14.83 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.073 / Rsym value: 0.073 / Net I/σ(I): 25.32 |
Reflection shell | Resolution: 1.51→1.54 Å / Rmerge(I) obs: 0.604 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 5314 / CC1/2: 0.725 / Rsym value: 0.604 / % possible all: 99.7 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.51→33.97 Å / SU ML: 0.1482 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.5182 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.51→33.97 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|