[English] 日本語
Yorodumi- PDB-3ksi: structure of fRMsr of Staphylococcus aureus (complex with 2-propanol) -
+Open data
-Basic information
Entry | Database: PDB / ID: 3ksi | ||||||
---|---|---|---|---|---|---|---|
Title | structure of fRMsr of Staphylococcus aureus (complex with 2-propanol) | ||||||
Components | Putative uncharacterized protein | ||||||
Keywords | OXIDOREDUCTASE / fRMsr / free-Met-R-SO | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Staphylococcus aureus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Bong, S.M. / Chi, Y.M. | ||||||
Citation | Journal: To be Published Title: structure of fRMsr of Staphylococcus aureus Authors: Bong, S.M. / Chi, Y.M. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3ksi.cif.gz | 45.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3ksi.ent.gz | 31 KB | Display | PDB format |
PDBx/mmJSON format | 3ksi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3ksi_validation.pdf.gz | 448.8 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 3ksi_full_validation.pdf.gz | 450.8 KB | Display | |
Data in XML | 3ksi_validation.xml.gz | 9.3 KB | Display | |
Data in CIF | 3ksi_validation.cif.gz | 12.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ks/3ksi ftp://data.pdbj.org/pub/pdb/validation_reports/ks/3ksi | HTTPS FTP |
-Related structure data
Related structure data | 3ksfC 1vhmS C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 17944.475 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus (bacteria) / Strain: MRSA252 / Gene: SAR1796 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q6GFY9, UniProt: A0A7U7EVB7*PLUS, L-methionine (R)-S-oxide reductase |
---|---|
#2: Chemical | ChemComp-IPA / |
#3: Chemical | ChemComp-SO4 / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.88 Å3/Da / Density % sol: 57.3 % |
---|---|
Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop Details: 2M ammonium sulfate, 10% isopropanol, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 4A / Wavelength: 1.2386 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Mar 31, 2008 |
Radiation | Monochromator: diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.2386 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→50 Å / Num. obs: 23645 / % possible obs: 94.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
-Processing
Software |
| ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1VHM Resolution: 1.7→44.92 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
| ||||||||||||||||||||
Solvent computation | Bsol: 53.444 Å2 | ||||||||||||||||||||
Displacement parameters | Biso mean: 23.891 Å2
| ||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.7→44.92 Å
| ||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||
LS refinement shell | Resolution: 1.7→1.81 Å / Rfactor Rfree error: 0.014
|