[English] 日本語
Yorodumi- PDB-3ld2: The Crystal Structure of smu.2055 from Streptococcus mutans UA159 -
+Open data
-Basic information
Entry | Database: PDB / ID: 3ld2 | ||||||
---|---|---|---|---|---|---|---|
Title | The Crystal Structure of smu.2055 from Streptococcus mutans UA159 | ||||||
Components | Putative acetyltransferase | ||||||
Keywords | TRANSFERASE / putative acetyltransferase | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Streptococcus mutans (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.5 Å | ||||||
Authors | Su, X.-D. / Zhan, X.R. / Gao, X.Z. / Liu, X. | ||||||
Citation | Journal: TO BE PUBLISHED Title: The Crystal Structure of smu.2055 from Streptococcus mutans UA159 Authors: Su, X.-D. / Zhan, X.R. / Gao, X.Z. / Liu, X. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3ld2.cif.gz | 137.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3ld2.ent.gz | 115.8 KB | Display | PDB format |
PDBx/mmJSON format | 3ld2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3ld2_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 3ld2_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 3ld2_validation.xml.gz | 30.6 KB | Display | |
Data in CIF | 3ld2_validation.cif.gz | 37.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ld/3ld2 ftp://data.pdbj.org/pub/pdb/validation_reports/ld/3ld2 | HTTPS FTP |
-Related structure data
Similar structure data |
---|
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
3 |
| ||||||||
4 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 22473.838 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus mutans (bacteria) / Strain: UA159 / Gene: smu.2055 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8DRZ8 #2: Chemical | ChemComp-COA / #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.34 Å3/Da / Density % sol: 47.34 % |
---|---|
Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 30% (v/v) pentaerythritol ethoxylate (15/4 EO/OH), 0.05M Bis-tris pH 6.5, 0.05M (NH4)2SO4, VAPOR DIFFUSION, SITTING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.9791 Å |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: May 31, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9791 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→50 Å / Num. all: 29608 / Num. obs: 29430 / % possible obs: 99.4 % / Observed criterion σ(I): 1 / Biso Wilson estimate: 34.79 Å2 |
Reflection shell | Resolution: 2.5→2.6 Å / % possible all: 96.9 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: SAD / Resolution: 2.5→19.998 Å / Occupancy max: 1 / Occupancy min: 0.8 / FOM work R set: 0.77 / SU ML: 0.42 / σ(F): 2.04 / Phase error: 29.27 / Stereochemistry target values: ML
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 38.226 Å2 / ksol: 0.35 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 86.61 Å2 / Biso mean: 25.128 Å2 / Biso min: 7.21 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→19.998 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|