+Open data
-Basic information
Entry | Database: PDB / ID: 6tud | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of Y. pestis penicillin-binding protein 3 | ||||||
Components | Peptidoglycan D,D-transpeptidase FtsI | ||||||
Keywords | CYTOSOLIC PROTEIN / Class B PBP / Yersinia pestis / HMM transpeptidase / periplasmic protein | ||||||
Function / homology | Function and homology information peptidoglycan glycosyltransferase activity / serine-type D-Ala-D-Ala carboxypeptidase / FtsZ-dependent cytokinesis / serine-type D-Ala-D-Ala carboxypeptidase activity / division septum assembly / penicillin binding / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / proteolysis / plasma membrane Similarity search - Function | ||||||
Biological species | Yersinia pestis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å | ||||||
Authors | Pankov, G. / Hunter, W.N. / Dawson, A. | ||||||
Citation | Journal: To Be Published Title: The structure of penicillin-binding protein 3 from Yersinia pestis Authors: Pankov, G. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6tud.cif.gz | 191.7 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6tud.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 6tud.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6tud_validation.pdf.gz | 442.6 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 6tud_full_validation.pdf.gz | 450.4 KB | Display | |
Data in XML | 6tud_validation.xml.gz | 32 KB | Display | |
Data in CIF | 6tud_validation.cif.gz | 43 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tu/6tud ftp://data.pdbj.org/pub/pdb/validation_reports/tu/6tud | HTTPS FTP |
-Related structure data
Related structure data | 6synSC 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: 59558.836 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Yersinia pestis (bacteria) / Gene: ftsI, YPO0549 / Production host: Escherichia coli (E. coli) References: UniProt: Q0WJB8, serine-type D-Ala-D-Ala carboxypeptidase #2: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.47 Å3/Da / Density % sol: 65 % |
---|---|
Crystal grow | Temperature: 296 K / Method: vapor diffusion, sitting drop Details: 1 uL of protein (in 20 mM Tris-HCl pH 7.5 150 mM NaCl and 2 mM carbenicillin) at 7 mg/ml and 0.2 uL of precipitant (0.2 M magnesium acetate, 6% gamma-PGA (Na+ form, LM) and 6% PEG8000) ...Details: 1 uL of protein (in 20 mM Tris-HCl pH 7.5 150 mM NaCl and 2 mM carbenicillin) at 7 mg/ml and 0.2 uL of precipitant (0.2 M magnesium acetate, 6% gamma-PGA (Na+ form, LM) and 6% PEG8000) Crystals were then dehydrated by replacing 50% of the reservoir solution with 50% PEG10000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9196 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jan 17, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9196 Å / Relative weight: 1 |
Reflection | Resolution: 3→29.64 Å / Num. obs: 33546 / % possible obs: 99.9 % / Redundancy: 10 % / Biso Wilson estimate: 50.6 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.2 / Rpim(I) all: 0.071 / Net I/σ(I): 9.1 |
Reflection shell | Resolution: 3→3.15 Å / Rmerge(I) obs: 1.099 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 4365 / CC1/2: 0.941 / Rpim(I) all: 0.518 / % possible all: 100 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6SYN Resolution: 3→29.64 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.91 / SU B: 26.209 / SU ML: 0.403 / Cross valid method: FREE R-VALUE / ESU R: 1.048 / ESU R Free: 0.398 Details: Hydrogens have been added in their riding positions
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 82.519 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3→29.64 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|