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Open data
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Basic information
Entry | Database: PDB / ID: 8ev5 | ||||||
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Title | NlpC B3 covalently bound with E64 inhibitor fragment | ||||||
![]() | Clan CA, family C40, NlpC/P60 superfamily cysteine peptidase | ||||||
![]() | HYDROLASE/Inhibitor / NlpC / P60 / CHAP / NlpC/P60 / Cysteine Protease / inhibitor / E64 / HYDROLASE / HYDROLASE-Inhibitor complex | ||||||
Function / homology | NlpC/P60 domain profile. / Endopeptidase, NLPC/P60 domain / NlpC/P60 family / Papain-like cysteine peptidase superfamily / Chem-E64 / Clan CA, family C40, NlpC/P60 superfamily cysteine peptidase![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Barnett, M.J. / Goldstone, D.C. | ||||||
Funding support | ![]()
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![]() | ![]() Title: NlpC/P60 peptidoglycan hydrolases of Trichomonas vaginalis have complementary activities that empower the protozoan to control host-protective lactobacilli. Authors: Barnett, M.J. / Pinheiro, J. / Keown, J.R. / Biboy, J. / Gray, J. / Lucinescu, I.W. / Vollmer, W. / Hirt, R.P. / Simoes-Barbosa, A. / Goldstone, D.C. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 39.6 KB | Display | ![]() |
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PDB format | ![]() | 24 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 8ev4C C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 13214.027 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Chemical | ChemComp-E64 / |
#3: Chemical | ChemComp-SO4 / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.98 Å3/Da / Density % sol: 37.89 % |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 1.26 M Ammonium Sulfate, 0.1 M Tris pH 8.5. / Temp details: (18 degrees Celsius) |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 27, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→33.43 Å / Num. obs: 13697 / % possible obs: 99.55 % / Redundancy: 2 % / Biso Wilson estimate: 18.45 Å2 / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.01579 / Rpim(I) all: 0.01579 / Rrim(I) all: 0.02232 / Net I/av σ(I): 15.48 / Net I/σ(I): 14.3 |
Reflection shell | Resolution: 1.65→1.709 Å / Redundancy: 2 % / Rmerge(I) obs: 0.2959 / Mean I/σ(I) obs: 2.01 / Num. unique obs: 2561 / CC1/2: 0.755 / CC star: 0.928 / Rpim(I) all: 0.2959 / Rrim(I) all: 0.4184 / % possible all: 95.68 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.977 Å2
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Refinement step | Cycle: 1 / Resolution: 1.65→33.43 Å
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Refine LS restraints |
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