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Open data
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Basic information
Entry | Database: PDB / ID: 3kxv | ||||||
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Title | Structure of complement Factor H variant Q1139A | ||||||
![]() | Complement factor H | ||||||
![]() | IMMUNE SYSTEM / Sushi domain / short consensus repeat domain / SCR domain / complement control protein module / complement regulator / atypical hemolytic uremic syndrome / renal disease / CFH / complement alternative pathway / disease mutation / glycoprotein / immune response / innate immunity | ||||||
Function / homology | ![]() regulation of complement activation, alternative pathway / symbiont cell surface / complement component C3b binding / regulation of complement-dependent cytotoxicity / regulation of complement activation / heparan sulfate proteoglycan binding / serine-type endopeptidase complex / complement activation, alternative pathway / complement activation / Regulation of Complement cascade ...regulation of complement activation, alternative pathway / symbiont cell surface / complement component C3b binding / regulation of complement-dependent cytotoxicity / regulation of complement activation / heparan sulfate proteoglycan binding / serine-type endopeptidase complex / complement activation, alternative pathway / complement activation / Regulation of Complement cascade / heparin binding / blood microparticle / proteolysis / extracellular space / extracellular exosome / extracellular region / identical protein binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Bhattacharjee, A. / Lehtinen, M.J. / Kajander, T. / Goldman, A. / Jokiranta, T.S. | ||||||
![]() | ![]() Title: Both domain 19 and domain 20 of factor H are involved in binding to complement C3b and C3d Authors: Bhattacharjee, A. / Lehtinen, M.J. / Kajander, T. / Goldman, A. / Jokiranta, T.S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 42.8 KB | Display | ![]() |
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PDB format | ![]() | 28.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 429.3 KB | Display | ![]() |
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Full document | ![]() | 429.7 KB | Display | |
Data in XML | ![]() | 8.3 KB | Display | |
Data in CIF | ![]() | 11 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3kzjC ![]() 2g7iS 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
#1: Protein | Mass: 15042.128 Da / Num. of mol.: 1 / Fragment: Sushi domains 19-20 / Mutation: Q1139A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() | ||
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#2: Chemical | ChemComp-SO4 / #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.07 Å3/Da / Density % sol: 69.81 % |
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Crystal grow | Temperature: 295.15 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 2M ammonium sulphate, 0.1M Bis-Tris buffer, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 295.15K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 3, 2007 |
Radiation | Monochromator: Diamond (111), Ge(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.931 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. obs: 16014 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.116 % / Biso Wilson estimate: 23.4 Å2 / Rsym value: 0.097 / Net I/σ(I): 16.8 |
Reflection shell | Resolution: 2→2.13 Å / Redundancy: 7.16 % / Mean I/σ(I) obs: 3.43 / Num. unique all: 18145 / Rsym value: 0.552 / % possible all: 98.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2G7I Resolution: 2.004→42.012 Å / Occupancy max: 1 / Occupancy min: 0.46 / FOM work R set: 0.844 / SU ML: 1.86 Isotropic thermal model: Isotropic individual temperature factors Cross valid method: THROUGHOUT / σ(F): 2 / Phase error: 22.27 / Stereochemistry target values: ML / Details: The structure was refined also with REFMAC 5.1
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 50.504 Å2 / ksol: 0.403 e/Å3 | |||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 82.04 Å2 / Biso mean: 25.159 Å2 / Biso min: 11.39 Å2
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Refinement step | Cycle: LAST / Resolution: 2.004→42.012 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6 / % reflection obs: 100 %
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