+Open data
-Basic information
Entry | Database: PDB / ID: 2y1z | ||||||
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Title | Human alphaB Crystallin ACD R120G | ||||||
Components | ALPHA-CRYSTALLIN B CHAINCRYAB | ||||||
Keywords | CHAPERONE / SMALL HEAT SHOCK PROTEIN / STRESS PROTEIN / EYE LENS PROTEIN / CATARACT | ||||||
Function / homology | Function and homology information 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 / muscle contraction / synaptic membrane / response to hydrogen peroxide / cellular response to gamma radiation / negative regulation of cell growth / Z disc / unfolded protein binding / protein folding / response to estradiol / amyloid-beta binding / response to heat / perikaryon / protein refolding / microtubule binding / dendritic spine / lysosome / response to hypoxia / protein stabilization / 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 / metal ion binding / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Clark, A.R. / Bagneris, C. / Naylor, C.E. / Keep, N.H. / Slingsby, C. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2011 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: Journal: J.Mol.Biol. / Year: 2009 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2y1z.cif.gz | 81.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2y1z.ent.gz | 62.3 KB | Display | PDB format |
PDBx/mmJSON format | 2y1z.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y1/2y1z ftp://data.pdbj.org/pub/pdb/validation_reports/y1/2y1z | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Ens-ID: 1 / Refine code: 6
NCS oper: (Code: given Matrix: (-0.996, -0.088, 0.032), Vector: |
-Components
#1: Protein | Mass: 10646.999 Da / Num. of mol.: 2 / Fragment: ALPHA-CRYSTALLIN DOMAIN (ACD), RESIDUES 67-157 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P02511 #2: Chemical | #3: Chemical | ChemComp-MPD / ( | #4: Water | ChemComp-HOH / | Compound details | ENGINEERED RESIDUE IN CHAIN A, ARG 120 TO HIS ENGINEERED RESIDUE IN CHAIN A, LEU 137 TO SER ...ENGINEERED | Sequence details | R120G IS A DISEASE ASSOCIATED MUTATION L137M TO ALLOW CRYSTALISATION. ALPHA-CRYSTALLIN DOMAIN ONLY. ...R120G IS A DISEASE ASSOCIATED | |
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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: 2.49 Å3/Da / Density % sol: 50.6 % / Description: NONE |
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Crystal grow | pH: 7.4 Details: PROTEIN AT 16.5 MG/ML IN BUFFER (25 MM TRISHCL, PH 7.5, 25 MM NACL) WAS MIXED 1:1 WITH MOTHER LIQUOR (36% MPD, 0.18M POTASSIUM CHLORIDE) |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.87 | |||||||||||||||
Detector | Type: ADSC CCD / Detector: CCD / Date: Jun 24, 2010 / Details: MIRRORS | |||||||||||||||
Radiation | Monochromator: CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength | Wavelength: 0.87 Å / Relative weight: 1 | |||||||||||||||
Reflection twin |
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Reflection | Resolution: 2.5→46.6 Å / Num. obs: 7582 / % possible obs: 98 % / Observed criterion σ(I): 2 / Redundancy: 9.2 % / Biso Wilson estimate: 43.7 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 19.4 | |||||||||||||||
Reflection shell | Resolution: 2.5→2.64 Å / Redundancy: 9.1 % / Rmerge(I) obs: 0.54 / Mean I/σ(I) obs: 4.3 / % possible all: 97.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: HUMAN ALPHA-CRYSTALLIN DOMAIN RESIDUES 71- 157 Resolution: 2.5→36.27 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.892 / SU B: 18.426 / SU ML: 0.189 / Cross valid method: THROUGHOUT / ESU R: 0.104 / ESU R Free: 0.06 / 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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.194 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→36.27 Å
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Refine LS restraints |
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