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Open data
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Basic information
Entry | Database: PDB / ID: 2y22 | ||||||
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Title | Human AlphaB-crystallin Domain (residues 67-157) | ||||||
![]() | ALPHA-CRYSTALLIN B | ||||||
![]() | CHAPERONE / SMALL HEAT SHOCK PROTEIN / STRESS PROTEIN / EYE LENS PROTEIN / CATARACT | ||||||
Function / homology | ![]() microtubule polymerization or depolymerization / negative regulation of intracellular transport / apoptotic process involved in morphogenesis / cardiac myofibril / regulation of programmed cell death / tubulin complex assembly / structural constituent of eye lens / negative regulation of amyloid fibril formation / M band / lens development in camera-type eye ...microtubule polymerization or depolymerization / negative regulation of intracellular transport / apoptotic process involved in morphogenesis / cardiac myofibril / regulation of programmed cell death / tubulin complex assembly / structural constituent of eye lens / negative regulation of amyloid fibril formation / M band / lens development in camera-type eye / muscle organ development / actin filament bundle / HSF1-dependent transactivation / negative regulation of reactive oxygen species metabolic process / negative regulation of protein-containing complex assembly / stress-activated MAPK cascade / synaptic membrane / muscle contraction / response to hydrogen peroxide / negative regulation of cell growth / cellular response to gamma radiation / Z disc / unfolded protein binding / protein folding / response to estradiol / amyloid-beta binding / response to heat / protein refolding / microtubule binding / perikaryon / dendritic spine / lysosome / protein stabilization / response to hypoxia / axon / negative regulation of gene expression / negative regulation of DNA-templated transcription / protein-containing complex binding / negative regulation of apoptotic process / structural molecule activity / cell surface / protein homodimerization activity / protein-containing complex / mitochondrion / extracellular exosome / nucleoplasm / identical protein binding / nucleus / metal ion binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Naylor, C.E. / Bagneris, C. / Clark, A.R. / Keep, N.H. / Slingsby, C. | ||||||
![]() | ![]() Title: Crystal Structure of R120G Disease Mutant of Human Alphab-Crystallin Domain Dimer Shows Closure of a Groove Authors: Clark, A.R. / Naylor, C.E. / Bagneris, C. / Keep, N.H. / Slingsby, C. #1: ![]() Title: Crystal Structures of Alpha-Crystallin Domain Dimers of Alphab-Crystallin and Hsp20. Authors: Bagneris, C. / Bateman, O.A. / Naylor, C.E. / Cronin, N. / Boelens, W.C. / Keep, N.H. / Slingsby, C. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 100.4 KB | Display | ![]() |
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PDB format | ![]() | 76.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 455.9 KB | Display | ![]() |
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Full document | ![]() | 457.9 KB | Display | |
Data in XML | ![]() | 16.2 KB | Display | |
Data in CIF | ![]() | 22.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2y1ySC ![]() 2y1zC C: citing same article ( 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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6 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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Components
#1: Protein | Mass: 10887.827 Da / Num. of mol.: 6 / Fragment: ALPHA-CRYSTALLIN DOMAIN (ACD), RESIDUES 67-157 / Mutation: YES Source method: isolated from a genetically manipulated source Details: SELENOMETHIONE CONTAINING PROTEIN / Source: (gene. exp.) ![]() ![]() ![]() Compound details | ENGINEERED RESIDUE IN CHAIN A, LEU 137 TO MET ENGINEERED RESIDUE IN CHAIN B, LEU 137 TO MET ...ENGINEERED | Sequence details | L 137 MUTATED TO METHIONINE | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.8 Å3/Da / Density % sol: 56 % / Description: NONE |
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Crystal grow | Method: vapor diffusion, sitting drop / pH: 9 Details: SITTING DROPS WITH 20 MG/ML PROTEIN IN 25 MM TRIS, PH 8.5, 200 MM NACL EQUILIBRATED AGAINST 110 MM BICINE, PH 9.0, 55% MPD |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC CCD / Detector: CCD / Date: Jun 25, 2008 / Details: MIRRORS |
Radiation | Monochromator: CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.978 Å / Relative weight: 1 |
Reflection | Resolution: 3.7→67.4 Å / Num. obs: 7861 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 12.8 % / Biso Wilson estimate: 56.13 Å2 / Rmerge(I) obs: 0.24 / Net I/σ(I): 8.7 |
Reflection shell | Resolution: 3.7→3.9 Å / Redundancy: 13.3 % / Rmerge(I) obs: 0.66 / Mean I/σ(I) obs: 4 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2Y1Y Resolution: 3.7→59.89 Å / Cor.coef. Fo:Fc: 0.8542 / Cor.coef. Fo:Fc free: 0.7946 / Cross valid method: THROUGHOUT / σ(F): 0 Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. ALL ATOMS HAVE CCP4 ATOM TYPE FROM LIBRARY
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Displacement parameters | Biso mean: 88.84 Å2
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Refine analyze | Luzzati coordinate error obs: 0.739 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.7→59.89 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.7→4.14 Å / Total num. of bins used: 5
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