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- PDB-6ryo: Bacterial membrane enzyme structure by the in meso method at 1.9 ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6ryo | |||||||||
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Title | Bacterial membrane enzyme structure by the in meso method at 1.9 A resolution | |||||||||
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![]() | HYDROLASE / in meso / Lipid cubic phases / lipoprotein signal peptidase / globomycin | |||||||||
Function / homology | ![]() signal peptidase II / aspartic-type endopeptidase activity / proteolysis / plasma membrane Similarity search - Function | |||||||||
Biological species | ![]() ![]() synthetic construct (others) | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Huang, C.Y. / Olatunji, S. / Bailey, J. / Yu, X. / Olieric, V. / Wang, M. / Caffrey, M. | |||||||||
Funding support | ![]() ![]()
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![]() | ![]() Title: Structures of lipoprotein signal peptidase II from Staphylococcus aureus complexed with antibiotics globomycin and myxovirescin. Authors: Olatunji, S. / Yu, X. / Bailey, J. / Huang, C.Y. / Zapotoczna, M. / Bowen, K. / Remskar, M. / Muller, R. / Scanlan, E.M. / Geoghegan, J.A. / Olieric, V. / Caffrey, M. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 98.2 KB | Display | ![]() |
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PDB format | ![]() | 71.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6rypC ![]() 5dirS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components
-Protein / Protein/peptide , 2 types, 2 molecules AB
#1: Protein | Mass: 21227.768 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Protein/peptide | Mass: 673.838 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
-Non-polymers , 5 types, 50 molecules ![](data/chem/img/OLC.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/7PE.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/7PE.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-OLC / ( #4: Chemical | ChemComp-GOL / #5: Chemical | ChemComp-7PE / #6: Chemical | ChemComp-ZN / | #7: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.45 Å3/Da / Density % sol: 49.7 % |
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Crystal grow | Temperature: 293 K / Method: lipidic cubic phase Details: 47.1 %(w/v) Polyethylene glycol 1,000, 150 mM Tris/HCl pH 8.0, 80 mM Potassium bromide |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 15, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.92003 Å / Relative weight: 1 |
Reflection | Resolution: 1.92→45.257 Å / Num. obs: 7046 / % possible obs: 86.2 % / Redundancy: 4.8 % / CC1/2: 0.99 / Rrim(I) all: 0.17 / Net I/σ(I): 7 |
Reflection shell | Resolution: 1.92→2.23 Å / Redundancy: 3.7 % / Mean I/σ(I) obs: 1.8 / Num. unique obs: 355 / CC1/2: 0.47 / Rrim(I) all: 1.38 / % possible all: 62.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5dir Resolution: 1.924→45.257 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 43.34
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.924→45.257 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 2.9893 Å / Origin y: 61.6516 Å / Origin z: 138.7238 Å
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Refinement TLS group | Selection details: all |