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Yorodumi- PDB-7n02: X-ray crystallographic structure model of Lactococcus lactis prol... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7n02 | ||||||
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Title | X-ray crystallographic structure model of Lactococcus lactis prolidase mutant D36S | ||||||
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 Xaa-Pro dipeptidase / proline dipeptidase activity / aminopeptidase activity / metal ion binding Similarity search - Function | ||||||
Biological species | Lactococcus lactis (lactic acid bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å | ||||||
Authors | Xu, S. / Grochulski, P. / Tanaka, T. | ||||||
Funding support | Canada, 1items
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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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7n02.cif.gz | 154.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7n02.ent.gz | 119.4 KB | Display | PDB format |
PDBx/mmJSON format | 7n02.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7n02_validation.pdf.gz | 1.8 MB | Display | wwPDB validaton report |
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Full document | 7n02_full_validation.pdf.gz | 1.8 MB | Display | |
Data in XML | 7n02_validation.xml.gz | 15.7 KB | Display | |
Data in CIF | 7n02_validation.cif.gz | 24.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n0/7n02 ftp://data.pdbj.org/pub/pdb/validation_reports/n0/7n02 | HTTPS FTP |
-Related structure data
Related structure data | 6xmrC 7k3uC 4zngS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 39985.289 Da / Num. of mol.: 2 / Mutation: D36S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lactococcus lactis (lactic acid bacteria) Gene: pepQ, AMHIJAGA_00052, BW151_08640, FNJ58_07375, GTP06_13345 Production host: Escherichia coli (E. coli) / References: UniProt: A8WBX8, Xaa-Pro dipeptidase #2: Chemical | ChemComp-MN / #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.71 Å3/Da / Density % sol: 54.57 % |
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Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, hanging drop Details: 0.1 M calcium acetate, 0.1 M Bis-Tris propane, 12-15% w/v PEG4000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: CLSI / Beamline: 08B1-1 / Wavelength: 1.5215 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jan 31, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5215 Å / Relative weight: 1 |
Reflection | Resolution: 2.35→43.64 Å / Num. obs: 36748 / % possible obs: 99.7 % / Redundancy: 6.1 % / CC1/2: 0.998 / Net I/σ(I): 11.8 |
Reflection shell | Resolution: 2.35→2.47 Å / Redundancy: 6.48 % / Num. unique obs: 3603 / CC1/2: 0.517 / % possible all: 99.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 4ZNG Resolution: 2.35→43.635 Å / SU ML: 0.53 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 37.72 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 112.21 Å2 / Biso mean: 57.6394 Å2 / Biso min: 34.79 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.35→43.635 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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