[English] 日本語
Yorodumi- PDB-7k3u: X-ray crystallographic structure model of Lactococcus lactis prol... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7k3u | ||||||
---|---|---|---|---|---|---|---|
Title | X-ray crystallographic structure model of Lactococcus lactis prolidase mutant R293S | ||||||
Components | Aminopeptidase P family protein | ||||||
Keywords | HYDROLASE / proline-specific / allosteric behaviour / substrate inhibition / dipeptidase / lactic acid bacteria / debittering of fermented foods | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Lactococcus lactis (lactic acid bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å | ||||||
Authors | Xu, S. / Grochulski, P. / Tanaka, T. | ||||||
Funding support | Canada, 1items
| ||||||
Citation | Journal: Biochim Biophys Acta Proteins Proteom / Year: 2017 Title: Crystallographic structure of recombinant Lactococcus lactis prolidase to support proposed structure-function relationships. Authors: Kgosisejo, O. / Chen, J.A. / Grochulski, P. / Tanaka, T. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 7k3u.cif.gz | 1.3 MB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb7k3u.ent.gz | 1.1 MB | Display | PDB format |
PDBx/mmJSON format | 7k3u.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7k3u_validation.pdf.gz | 7.5 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 7k3u_full_validation.pdf.gz | 7.6 MB | Display | |
Data in XML | 7k3u_validation.xml.gz | 145 KB | Display | |
Data in CIF | 7k3u_validation.cif.gz | 198 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k3/7k3u ftp://data.pdbj.org/pub/pdb/validation_reports/k3/7k3u | HTTPS FTP |
-Related structure data
Related structure data | 6xmrC 7n02C 4zngS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
3 |
| ||||||||
4 |
| ||||||||
5 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 39943.184 Da / Num. of mol.: 10 / Mutation: R293S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lactococcus lactis (lactic acid bacteria) Gene: pepQ, AMHIJAGA_00052, BW151_08640, FNJ58_07375 / Production host: Escherichia coli (E. coli) / References: UniProt: A8WBX8, Xaa-Pro dipeptidase #2: Chemical | ChemComp-MN / #3: Chemical | ChemComp-GOL / #4: 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: 2.68 Å3/Da / Density % sol: 54.13 % |
---|---|
Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.1 M calcium acetate, 0.1 M Bis-Tris propane, 15% w/v PEG4000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 30, 2019 |
Radiation | Monochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97949 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→49.19 Å / Num. obs: 116597 / % possible obs: 99.7 % / Redundancy: 3.4 % / CC1/2: 0.998 / Net I/σ(I): 10.8 |
Reflection shell | Resolution: 2.7→2.8 Å / Num. unique obs: 11587 / CC1/2: 0.845 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 4ZNG Resolution: 2.7→49.19 Å / SU ML: 0.48 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 32.62 / Stereochemistry target values: ML
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 195.72 Å2 / Biso mean: 65.9243 Å2 / Biso min: 26.98 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.7→49.19 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Origin x: -91.1986 Å / Origin y: -27.9509 Å / Origin z: -47.2757 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|