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Open data
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Basic information
Entry | Database: PDB / ID: 2j8b | ||||||
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Title | High resolution structure of human CD59 | ||||||
![]() | CD59 GLYCOPROTEIN | ||||||
![]() | LIPID BINDING PROTEIN / LIPID-BINDING PROTEIN / GLYCOPROTEIN / LIPID-BINDING PROTEIN MAC / MEMBRANE / GPI-ANCHOR / COMPLEMENT / LIPOPROTEIN | ||||||
Function / homology | ![]() negative regulation of activation of membrane attack complex / complement binding / regulation of complement-dependent cytotoxicity / regulation of complement activation / Cargo concentration in the ER / COPII-mediated vesicle transport / tertiary granule membrane / COPI-mediated anterograde transport / specific granule membrane / transport vesicle ...negative regulation of activation of membrane attack complex / complement binding / regulation of complement-dependent cytotoxicity / regulation of complement activation / Cargo concentration in the ER / COPII-mediated vesicle transport / tertiary granule membrane / COPI-mediated anterograde transport / specific granule membrane / transport vesicle / endoplasmic reticulum-Golgi intermediate compartment membrane / Regulation of Complement cascade / ER to Golgi transport vesicle membrane / blood coagulation / vesicle / cell surface receptor signaling pathway / external side of plasma membrane / Golgi membrane / focal adhesion / Neutrophil degranulation / endoplasmic reticulum membrane / cell surface / extracellular space / extracellular exosome / membrane / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Leath, K.J. / Johnson, S. / Roversi, P. / Morgan, B.P. / Smith, R.A.G. / Lea, S.M. | ||||||
![]() | ![]() Title: High-Resolution Structures of Bacterially Expressed Soluble Human Cd59. Authors: Leath, K.J. / Johnson, S. / Roversi, P. / Hughes, T.R. / Smith, R.A.G. / Mackenzie, L. / Morgan, B.P. / Lea, S.M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 51.1 KB | Display | ![]() |
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PDB format | ![]() | 36.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 410.1 KB | Display | ![]() |
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Full document | ![]() | 410.6 KB | Display | |
Data in XML | ![]() | 6.7 KB | Display | |
Data in CIF | ![]() | 8.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2uwrC ![]() 2ux2C ![]() 1cdqS 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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Unit cell |
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Components
#1: Protein | Mass: 9158.354 Da / Num. of mol.: 1 / Fragment: MATURE POLYPEPTIDE, RESIDUES 26-103 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Description: PURIFIED FROM INCLUSION BODIES AFTER EXPRESSION IN ESCHERICHIA COLI Cell: LYMPHOCYTES, ERYTHROCYTES, PLATELETS, ENDOTHELIA, EPITHELIA Plasmid: PET59-06 / Production host: ![]() ![]() |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.84 Å3/Da / Density % sol: 33 % / Description: NONE |
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Crystal grow | Details: 28 % PEG 4000 0.25M AMMONIUM SULPHATE |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||
Detector | Type: ADSC CCD / Detector: CCD / Date: May 21, 2006 | |||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||
Radiation wavelength |
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Reflection | Resolution: 1.1→26.2 Å / Num. obs: 27724 / % possible obs: 99 % / Observed criterion σ(I): 0 / Redundancy: 12 % / Biso Wilson estimate: 8.4 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 20.7 | |||||||||
Reflection shell | Resolution: 1.1→1.16 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.24 / Mean I/σ(I) obs: 3.7 / % possible all: 93.3 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1CDQ Resolution: 1.15→20 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.949 / SU B: 1.043 / SU ML: 0.023 / Cross valid method: THROUGHOUT / ESU R: 0.042 / ESU R Free: 0.042 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUE 78 WAS NOT MODELLED
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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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 12.96 Å2
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Refinement step | Cycle: LAST / Resolution: 1.15→20 Å
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Refine LS restraints |
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