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- PDB-8w18: The crystal structure of the Michaelis-Menten complex of a C1s/C1... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8w18 | ||||||
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Title | The crystal structure of the Michaelis-Menten complex of a C1s/C1-INH at 3.94 Angstroms | ||||||
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![]() | IMMUNE SYSTEM / complement / C1s / C1 esterase inhibitor / Michaelis complex / reactive center loop / exosite | ||||||
Function / homology | ![]() complement subcomponent C_overbar_1s_ / negative regulation of complement activation, lectin pathway / Defective SERPING1 causes hereditary angioedema / blood circulation / Classical antibody-mediated complement activation / Initial triggering of complement / fibrinolysis / Intrinsic Pathway of Fibrin Clot Formation / platelet alpha granule lumen / complement activation, classical pathway ...complement subcomponent C_overbar_1s_ / negative regulation of complement activation, lectin pathway / Defective SERPING1 causes hereditary angioedema / blood circulation / Classical antibody-mediated complement activation / Initial triggering of complement / fibrinolysis / Intrinsic Pathway of Fibrin Clot Formation / platelet alpha granule lumen / complement activation, classical pathway / Regulation of Complement cascade / serine-type endopeptidase inhibitor activity / blood coagulation / Platelet degranulation / collagen-containing extracellular matrix / blood microparticle / endoplasmic reticulum lumen / serine-type endopeptidase activity / innate immune response / calcium ion binding / proteolysis / extracellular space / extracellular exosome / extracellular region / identical protein binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Garrigues, R.J. / Garcia, B.L. | ||||||
Funding support | ![]()
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![]() | ![]() Title: The crystal structure of the Michaelis-Menten complex of a C1s/C1-INH Authors: Garrigues, R.J. / Garrison, M.P. / Garcia, B.L. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 178.5 KB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 446.2 KB | Display | ![]() |
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Full document | ![]() | 459.3 KB | Display | |
Data in XML | ![]() | 28.9 KB | Display | |
Data in CIF | ![]() | 38.5 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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Unit cell |
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Components
#1: Protein | Mass: 43997.434 Da / Num. of mol.: 1 / Fragment: residues 111-500 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Protein | Mass: 27668.547 Da / Num. of mol.: 1 / Mutation: S632A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
#3: Protein | Mass: 16588.488 Da / Num. of mol.: 1 / Fragment: Sushi domains Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.56 Å3/Da / Density % sol: 65.43 % / Description: blocks |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop Details: 0.1 M L-Proline, 0.1M HEPES (pH 6.5), and 12% PEG 3,350 |
-Data collection
Diffraction | Mean temperature: 93 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 15, 2023 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3.94→49.42 Å / Num. obs: 11775 / % possible obs: 100 % / Redundancy: 12.8 % / Biso Wilson estimate: 145.32 Å2 / CC1/2: 0.996 / Rpim(I) all: 0.127 / Net I/σ(I): 6.9 |
Reflection shell | Resolution: 3.94→4.15 Å / Redundancy: 12.9 % / Mean I/σ(I) obs: 1.1 / Num. unique obs: 3267 / CC1/2: 0.446 / Rpim(I) all: 0.776 / % possible all: 100 |
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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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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 161.56 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.94→47.42 Å
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Refine LS restraints |
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LS refinement shell |
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