+Open data
-Basic information
Entry | Database: PDB / ID: 3l1f | ||||||
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Title | Bovine AlphaA crystallin | ||||||
Components | Alpha-crystallin A chain | ||||||
Keywords | CHAPERONE / lens transparency / polydispersity / protein aggregation / crystallin / Eye lens protein | ||||||
Function / homology | Function and homology information negative regulation of intracellular transport / structural constituent of eye lens / lens development in camera-type eye / visual perception / unfolded protein binding / response to heat / protein stabilization / negative regulation of apoptotic process / protein-containing complex / nucleoplasm ...negative regulation of intracellular transport / structural constituent of eye lens / lens development in camera-type eye / visual perception / unfolded protein binding / response to heat / protein stabilization / negative regulation of apoptotic process / protein-containing complex / nucleoplasm / identical protein binding / metal ion binding / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Bos taurus (cattle) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.53 Å | ||||||
Authors | Laganowsky, A. / Sawaya, M.R. / Cascio, D. / Eisenberg, D. | ||||||
Citation | Journal: Protein Sci. / Year: 2010 Title: Crystal structures of truncated alphaA and alphaB crystallins reveal structural mechanisms of polydispersity important for eye lens function. Authors: Laganowsky, A. / Benesch, J.L. / Landau, M. / Ding, L. / Sawaya, M.R. / Cascio, D. / Huang, Q. / Robinson, C.V. / Horwitz, J. / Eisenberg, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3l1f.cif.gz | 54.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3l1f.ent.gz | 38.6 KB | Display | PDB format |
PDBx/mmJSON format | 3l1f.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l1/3l1f ftp://data.pdbj.org/pub/pdb/validation_reports/l1/3l1f | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 11658.912 Da / Num. of mol.: 1 / Fragment: residues 62-163 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bos taurus (cattle) / Gene: CRYA1, CRYAA / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P02470 |
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#2: Chemical | ChemComp-MPD / ( |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.35 Å3/Da / Density % sol: 47.55 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.1M HEPES pH 7.5, 10% PEG 6000, 5% MPD, vapor diffusion, sitting drop, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 9, 2009 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.53→80 Å / Num. obs: 16465 / % possible obs: 94.9 % / Redundancy: 6.8 % / Rmerge(I) obs: 0.041 / Χ2: 1.055 / Net I/σ(I): 16.6 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.53→29.462 Å / Occupancy max: 1 / Occupancy min: 0.13 / FOM work R set: 0.897 / SU ML: 0.18 / σ(F): 0.07 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60.825 Å2 / ksol: 0.4 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 62.47 Å2 / Biso mean: 28.624 Å2 / Biso min: 13.75 Å2
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Refine analyze | Luzzati sigma a obs: 0.18 Å | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.53→29.462 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
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