[English] 日本語
Yorodumi- PDB-4la3: Crystal structure of dimethylsulphoniopropionate (DMSP) lyase Ddd... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4la3 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of dimethylsulphoniopropionate (DMSP) lyase DddQ Y131A in complex with DMSP | ||||||
Components | Dimethylsulphoniopropionate (DMSP) lyase DddQ | ||||||
Keywords | LYASE / Cupin motif / DMSP lyase | ||||||
Function / homology | Function and homology information dimethylpropiothetin dethiomethylase / dimethylpropiothetin dethiomethylase activity / metal ion binding Similarity search - Function | ||||||
Biological species | Silicibacter lacuscaerulensis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.701 Å | ||||||
Authors | Zhang, Y. / Li, C. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2014 Title: Molecular insight into bacterial cleavage of oceanic dimethylsulfoniopropionate into dimethyl sulfide Authors: Li, C. / Wei, T. / Zhang, S. / Chen, X. / Gao, X. / Wang, P. / Xie, B. / Su, H. / Qin, Q. / Zhang, X. / Yu, J. / Zhang, H. / Zhou, B. / Yang, G. / Zhang, Y. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4la3.cif.gz | 158.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4la3.ent.gz | 125.5 KB | Display | PDB format |
PDBx/mmJSON format | 4la3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4la3_validation.pdf.gz | 462.4 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 4la3_full_validation.pdf.gz | 469.9 KB | Display | |
Data in XML | 4la3_validation.xml.gz | 17 KB | Display | |
Data in CIF | 4la3_validation.cif.gz | 22 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/la/4la3 ftp://data.pdbj.org/pub/pdb/validation_reports/la/4la3 | HTTPS FTP |
-Related structure data
Related structure data | 4la2SC S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 21929.434 Da / Num. of mol.: 2 / Mutation: Y131A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Silicibacter lacuscaerulensis (bacteria) Strain: ITI-1157 / Gene: SL1157_0332 / Production host: Escherichia coli (E. coli) / References: UniProt: D0CY60 #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
---|
-Sample preparation
Crystal | Density Matthews: 2.01 Å3/Da / Density % sol: 38.71 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 0.2M sodium chloride, 0.1M MES, 20% (w/v) PEG 2000 MME , pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9793 Å | |||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: May 13, 2013 | |||||||||
Radiation | Monochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 | |||||||||
Reflection | Resolution: 2.7→50 Å / Num. obs: 10119 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 40.65 Å2 | |||||||||
Reflection shell |
|
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4LA2 Resolution: 2.701→42.325 Å / Occupancy max: 1 / Occupancy min: 0.63 / FOM work R set: 0.7416 / SU ML: 0.35 / σ(F): 0 / Phase error: 30.58 / Stereochemistry target values: Overall
| ||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 34.084 Å2 / ksol: 0.374 e/Å3 | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 104.88 Å2 / Biso mean: 46.596 Å2 / Biso min: 22.57 Å2
| ||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.701→42.325 Å
| ||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 3
| ||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Origin x: 24.2134 Å / Origin y: -11.586 Å / Origin z: -20.621 Å
| ||||||||||||||||||||||||||||||||||||||||
Refinement TLS group | Selection details: all |