+Open data
-Basic information
Entry | Database: PDB / ID: 5jcv | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Sortase B from Listeria monocytogenes. | |||||||||
Components | Lmo2181 protein | |||||||||
Keywords | HYDROLASE / sortase / structural genomics / Center for Structural Genomics of Infectious Diseases / CSGID | |||||||||
Function / homology | Function and homology information cellular response to iron ion / membrane => GO:0016020 / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / hydrolase activity / plasma membrane Similarity search - Function | |||||||||
Biological species | Listeria monocytogenes serovar 1/2a (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.23 Å | |||||||||
Authors | Osipiuk, J. / Zhou, M. / Grimshaw, S. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID) | |||||||||
Funding support | United States, 2items
| |||||||||
Citation | Journal: to be published Title: Sortase B from Listeria monocytogenes. Authors: Osipiuk, J. / Zhou, M. / Grimshaw, S. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID) | |||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5jcv.cif.gz | 85.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5jcv.ent.gz | 68.9 KB | Display | PDB format |
PDBx/mmJSON format | 5jcv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5jcv_validation.pdf.gz | 435.8 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 5jcv_full_validation.pdf.gz | 436.3 KB | Display | |
Data in XML | 5jcv_validation.xml.gz | 8.7 KB | Display | |
Data in CIF | 5jcv_validation.cif.gz | 10.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jc/5jcv ftp://data.pdbj.org/pub/pdb/validation_reports/jc/5jcv | HTTPS FTP |
-Related structure data
Similar structure data | |
---|---|
Other databases |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 21754.641 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Listeria monocytogenes serovar 1/2a (strain ATCC BAA-679 / EGD-e) (bacteria) Strain: ATCC BAA-679 / EGD-e / Gene: lmo2181 / Plasmid: pMCSG53 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8Y588 |
---|---|
#2: Chemical | ChemComp-SO4 / |
#3: Chemical | ChemComp-CL / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.32 Å3/Da / Density % sol: 62.97 % |
---|---|
Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 0.2 M lithium sulfate, 2 M ammonium sulfate, 0.1 M Tris-Cl |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9792 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 18, 2015 |
Radiation | Monochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 2.23→33.6 Å / Num. obs: 14055 / % possible obs: 99.2 % / Redundancy: 10.9 % / Rmerge(I) obs: 0.087 / Net I/av σ(I): 11.1 / Net I/σ(I): 36.4 |
Reflection shell | Resolution: 2.23→2.27 Å / Redundancy: 10.8 % / Rmerge(I) obs: 0.89 / Mean I/σ(I) obs: 2.88 / % possible all: 100 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: SAD / Resolution: 2.23→33.6 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.931 / SU B: 13.423 / SU ML: 0.156 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.211 / ESU R Free: 0.189 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 142.57 Å2 / Biso mean: 65.891 Å2 / Biso min: 37.77 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.23→33.6 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.233→2.29 Å / Total num. of bins used: 20
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Origin x: 17.2656 Å / Origin y: -1.8639 Å / Origin z: 67.2407 Å
|