+Open data
-Basic information
Entry | Database: PDB / ID: 2ux2 | ||||||
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Title | High resolution structure of human CD59 | ||||||
Components | CD59 GLYCOPROTEIN | ||||||
Keywords | IMMUNE SYSTEM / MAC / MIRL / CD59 / MEMBRANE / GPI-ANCHOR / LIPOPROTEIN / GLYCOPROTEIN / COMPLEMENT REGULATOR | ||||||
Function / homology | Function and homology information 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 | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Leath, K.J. / Johnson, S. / Roversi, P. / Morgan, B.P. / Smith, R.A.G. / Lea, S.M. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.F / Year: 2007 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2ux2.cif.gz | 62.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ux2.ent.gz | 46.7 KB | Display | PDB format |
PDBx/mmJSON format | 2ux2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2ux2_validation.pdf.gz | 431.1 KB | Display | wwPDB validaton report |
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Full document | 2ux2_full_validation.pdf.gz | 432.3 KB | Display | |
Data in XML | 2ux2_validation.xml.gz | 12.9 KB | Display | |
Data in CIF | 2ux2_validation.cif.gz | 17.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ux/2ux2 ftp://data.pdbj.org/pub/pdb/validation_reports/ux/2ux2 | HTTPS FTP |
-Related structure data
Related structure data | 2j8bC 2uwrC 2j8cS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
#1: Protein | Mass: 9101.303 Da / Num. of mol.: 3 / Fragment: RESIDUES 26-102 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PET59-06 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): UT5600 DE3 / References: UniProt: P13987 #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.13 Å3/Da / Density % sol: 42 % / Description: NONE |
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Crystal grow | Details: 25% PEG8000, 0.03M POTASSIUM PHOSPHATE |
-Data collection
Diffraction | Mean temperature: 77 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.24 |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: May 20, 2006 |
Radiation | Monochromator: SI MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.24 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→40 Å / Num. obs: 20934 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 14.3 % / Biso Wilson estimate: 0.65 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 29 |
Reflection shell | Resolution: 1.8→1.9 Å / Redundancy: 14.1 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 7 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2J8C Resolution: 1.8→20 Å / Isotropic thermal model: TNT BCORREL / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: TNT PROTEGO
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Solvent computation | Solvent model: BABINET SCALING / Bsol: 107 Å2 / ksol: 0.49 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→20 Å
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Refine LS restraints |
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