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Open data
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Basic information
Entry | Database: PDB / ID: 2oay | ||||||
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Title | Crystal structure of latent human C1-inhibitor | ||||||
![]() | Plasma protease C1 inhibitor | ||||||
![]() | IMMUNE SYSTEM / HYDROLASE INHIBITOR / LATENT SERPIN / RCL INSERTION | ||||||
Function / homology | ![]() negative regulation of complement activation, lectin pathway / Defective SERPING1 causes hereditary angioedema / blood circulation / 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 ...negative regulation of complement activation, lectin pathway / Defective SERPING1 causes hereditary angioedema / blood circulation / 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 / innate immune response / extracellular space / extracellular exosome / extracellular region Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Harmat, V. / Beinrohr, L. / Gal, P. / Dobo, J. | ||||||
![]() | ![]() Title: C1 inhibitor serpin domain structure reveals the likely mechanism of heparin potentiation and conformational disease Authors: Beinrohr, L. / Harmat, V. / Dobo, J. / Lorincz, Z. / Gal, P. / Zavodszky, P. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 89.5 KB | Display | ![]() |
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PDB format | ![]() | 65.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 467.2 KB | Display | ![]() |
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Full document | ![]() | 472.9 KB | Display | |
Data in XML | ![]() | 16.5 KB | Display | |
Data in CIF | ![]() | 22.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1c8oS ![]() 1dvmS ![]() 1e05S ![]() 1hleS ![]() 1jjoS ![]() 1jrrS ![]() 1jtiS ![]() 1mtpS ![]() 1qmbS ![]() 4caaS 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
#1: Protein | Mass: 43903.484 Da / Num. of mol.: 1 / Fragment: serpin domain / Mutation: allele V458M Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() | ||
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#2: Sugar | ChemComp-NAG / | ||
#3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.04 Å3/Da / Density % sol: 59.59 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.85 M NaH2PO4, 0.85 M KH2PO4, 0.1 M HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: May 3, 2006 / Details: mirrors |
Radiation | Monochromator: Si [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8162 Å / Relative weight: 1 |
Reflection | Resolution: 2.35→84.52 Å / Num. obs: 21930 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 14.6 % / Biso Wilson estimate: 32.4 Å2 / Rmerge(I) obs: 0.097 / Net I/σ(I): 20.29 |
Reflection shell | Resolution: 2.35→2.4 Å / Redundancy: 9.54 % / Rmerge(I) obs: 0.652 / Mean I/σ(I) obs: 3.89 / Num. unique all: 1341 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: Ensemble of truncated serpin structures. PDB codes: 4CAA, 1QMB, 1E05, 1DVM, 1C8O, 1JTI, 1JJO, 1MTP, 1HLE, 1JRR Resolution: 2.35→84.52 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.948 / SU B: 6.574 / SU ML: 0.154 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.239 / ESU R Free: 0.197 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.433 Å2
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Refinement step | Cycle: LAST / Resolution: 2.35→84.52 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.35→2.411 Å / Total num. of bins used: 20 /
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Refinement TLS params. | Method: refined / Origin x: -14.7946 Å / Origin y: 71.6738 Å / Origin z: -0.6784 Å
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Refinement TLS group |
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