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- PDB-7bb8: Crystal structure of Lugdulysin, a Staphylococcus lugdunensis M30... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7bb8 | ||||||
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Title | Crystal structure of Lugdulysin, a Staphylococcus lugdunensis M30 zinc metallopeptidase | ||||||
![]() | Neutral metalloprotease | ||||||
![]() | HYDROLASE / Protease / Virulence factor / peptidase | ||||||
Function / homology | Peptidase M30, hyicolysin / Peptidase M30 / metallopeptidase activity / proteolysis / ACETATE ION / CACODYLATE ION / Neutral metalloprotease![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Ruff, M. / Prevost, G. / Prola, K. / Levy, N. | ||||||
![]() | ![]() Title: Crystal structure of Staphylococcus lugdunensis protease, Lugdulysin Authors: Ruff, M. / Prevost, G. / Prola, K. / Levy, N. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 473.1 KB | Display | ![]() |
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PDB format | ![]() | 377.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 450.2 KB | Display | ![]() |
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Full document | ![]() | 451.3 KB | Display | |
Data in XML | ![]() | 35.6 KB | Display | |
Data in CIF | ![]() | 56.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 47210.430 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
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-Non-polymers , 5 types, 948 molecules ![](data/chem/img/ZN.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/CAC.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/CAC.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | ChemComp-CA / #4: Chemical | ChemComp-CAC / | #5: Chemical | ChemComp-ACT / | #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.8 Å3/Da / Density % sol: 55.99 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.1M Sodium Cacodylate pH 6.5; 30% PEG 8000; 0.2 M Sodium acetate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() |
Detector | Type: DECTRIS EIGER R 4M / Detector: PIXEL / Date: Jul 28, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.506→39.77 Å / Num. obs: 162434 / % possible obs: 95.81 % / Redundancy: 5.4 % / CC1/2: 0.999 / Rrim(I) all: 0.063 / Net I/σ(I): 12.35 |
Reflection shell | Resolution: 1.506→1.56 Å / Redundancy: 1.4 % / Num. unique obs: 14979 / CC1/2: 0.264 / % possible all: 62.73 |
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Processing
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Refinement | Method to determine structure: ![]() Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Displacement parameters | Biso mean: 31.29 Å2 | ||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.506→39.77 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.506→1.56 Å / Rfactor Rfree: 0.4157 / Rfactor Rwork: 0.4012 |