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- PDB-5ncu: Structure of the subtilisin induced serpin-type proteinase inhibi... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5ncu | |||||||||||||||||||||
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Title | Structure of the subtilisin induced serpin-type proteinase inhibitor, miropin. | |||||||||||||||||||||
![]() | (Serpin) x 2 | |||||||||||||||||||||
![]() | HYDROLASE INHIBITOR / Serpin-type proteinase inhibitor | |||||||||||||||||||||
Function / homology | ![]() serine-type endopeptidase inhibitor activity / extracellular space / metal ion binding Similarity search - Function | |||||||||||||||||||||
Biological species | ![]() | |||||||||||||||||||||
Method | ![]() ![]() ![]() | |||||||||||||||||||||
![]() | Goulas, T. / Ksiazek, M. / Garcia-Ferrer, I. / Mizgalska, D. / Potempa, J. / Gomis-Ruth, X. | |||||||||||||||||||||
Funding support | ![]()
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![]() | ![]() Title: A structure-derived snap-trap mechanism of a multispecific serpin from the dysbiotic human oral microbiome. Authors: Goulas, T. / Ksiazek, M. / Garcia-Ferrer, I. / Sochaj-Gregorczyk, A.M. / Waligorska, I. / Wasylewski, M. / Potempa, J. / Gomis-Ruth, F.X. | |||||||||||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 169.3 KB | Display | ![]() |
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PDB format | ![]() | 131.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5ncsC ![]() 5nctC ![]() 5ncwC ![]() 1hleS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-Protein / Protein/peptide , 2 types, 2 molecules AB
#1: Protein | Mass: 37705.094 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: The amino-terminal residues (GPLGS) are coming from the cloning strategy. Where CSX is S-Oxy cysteine. Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Protein/peptide | Mass: 4308.948 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: The amino-terminal residues (GPLGS) are coming from the cloning strategy. Where CSX is S-Oxy cysteine. Source: (gene. exp.) ![]() ![]() ![]() |
-Non-polymers , 5 types, 414 molecules ![](data/chem/img/K.gif)
![](data/chem/img/IOD.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/IOD.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-K / | ||||||
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#4: Chemical | ChemComp-IOD / #5: Chemical | ChemComp-CL / | #6: Chemical | ChemComp-GOL / #7: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.42 Å3/Da / Density % sol: 49.27 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7.4 Details: 200 mM sodium iodide 100 mM Bis-Tris, pH 6.5 20% [w/v] polyethylene glycol 3,350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 28, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→55.5 Å / Num. obs: 45392 / % possible obs: 99.5 % / Redundancy: 12.1 % / Biso Wilson estimate: 24.51 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.051 / Rrim(I) all: 0.054 / Net I/σ(I): 29.9 |
Reflection shell | Resolution: 1.7→1.8 Å / Redundancy: 7.6 % / Rmerge(I) obs: 0.479 / Mean I/σ(I) obs: 4.4 / Num. unique all: 3127 / Num. unique obs: 3127 / CC1/2: 0.931 / Rrim(I) all: 0.513 / % possible all: 96.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1HLE Resolution: 1.7→24.89 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.948 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.089 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.097 / SU Rfree Blow DPI: 0.089 / SU Rfree Cruickshank DPI: 0.085
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Displacement parameters | Biso mean: 29.09 Å2
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Refine analyze | Luzzati coordinate error obs: 0.19 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 1.7→24.89 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.74 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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