[English] 日本語
Yorodumi- PDB-6xv5: Crystal structure of penicillin-binding protein 2 from Yersinia p... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6xv5 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of penicillin-binding protein 2 from Yersinia pestis in complex with ertapenem | ||||||
Components | Peptidoglycan D,D-transpeptidase MrdA | ||||||
Keywords | MEMBRANE PROTEIN / Class B PBP / Yersinia pestis / HMM transpeptidase / periplasmic protein / peptidoglycan crosslinking / ertapenem | ||||||
Function / homology | Function and homology information peptidoglycan L,D-transpeptidase activity / serine-type D-Ala-D-Ala carboxypeptidase / serine-type D-Ala-D-Ala carboxypeptidase activity / 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: 2.673 Å | ||||||
Authors | Pankov, G. / Hunter, W.N. / Dawson, A. | ||||||
Citation | Journal: To Be Published Title: The structure of penicillin-binding protein 2 from Yersinia pestis Authors: Pankov, G. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6xv5.cif.gz | 235.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6xv5.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 6xv5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6xv5_validation.pdf.gz | 467.4 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 6xv5_full_validation.pdf.gz | 485.6 KB | Display | |
Data in XML | 6xv5_validation.xml.gz | 42.3 KB | Display | |
Data in CIF | 6xv5_validation.cif.gz | 56.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xv/6xv5 ftp://data.pdbj.org/pub/pdb/validation_reports/xv/6xv5 | HTTPS FTP |
-Related structure data
Related structure data | 6tiiSC S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
| ||||||||
Noncrystallographic symmetry (NCS) | NCS domain: (Details: Chains BBB AAA) |
-Components
#1: Protein | Mass: 66012.406 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Yersinia pestis (bacteria) / Gene: mrdA, YPO2604 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: A0A384KFW3, serine-type D-Ala-D-Ala carboxypeptidase #2: Chemical | ChemComp-TLA / | #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.59 Å3/Da / Density % sol: 52.49 % |
---|---|
Crystal grow | Temperature: 296 K / Method: vapor diffusion Details: Crystals were grown in a condition containing 1 uL of 1 mg/mL YpPBP2 (in 20 mM Tris-HCl pH 7.5, 150 mM NaCl, 2 mM ertapenem) and 2 uL of reservoir solution (0.5 M Na+/K+ tartrate, 0.1 M HEPES-NaOH pH 7.5). |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 9, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.67→109.937 Å / Num. obs: 38541 / % possible obs: 100 % / Redundancy: 13.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.133 / Net I/σ(I): 12.2 |
Reflection shell | Resolution: 2.701→7.331 Å / Rmerge(I) obs: 0.04 / Num. unique obs: 2108 / CC1/2: 0.999 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6TII Resolution: 2.673→109.937 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.883 / SU B: 18.456 / SU ML: 0.351 / Cross valid method: FREE R-VALUE / ESU R Free: 0.461
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 77.799 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.673→109.937 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20
|