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- PDB-3l1g: Human AlphaB crystallin -

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Basic information

Entry
Database: PDB / ID: 3l1g
TitleHuman AlphaB crystallin
ComponentsAlpha-crystallin B chainCRYAB
KeywordsCHAPERONE / lens transparency / polydispersity / protein aggregation / crystallin / Eye lens protein
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
Alpha-crystallin B chain, ACD domain / Alpha-crystallin, N-terminal / Alpha crystallin A chain, N terminal / Alpha crystallin/Small heat shock protein, animal type / Immunoglobulin-like - #790 / Hsp20/alpha crystallin family / Small heat shock protein (sHSP) domain profile. / Alpha crystallin/Hsp20 domain / HSP20-like chaperone / Immunoglobulin-like ...Alpha-crystallin B chain, ACD domain / Alpha-crystallin, N-terminal / Alpha crystallin A chain, N terminal / Alpha crystallin/Small heat shock protein, animal type / Immunoglobulin-like - #790 / Hsp20/alpha crystallin family / Small heat shock protein (sHSP) domain profile. / Alpha crystallin/Hsp20 domain / HSP20-like chaperone / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Alpha-crystallin B chain
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.32 Å
AuthorsLaganowsky, A. / Sawaya, M.R. / Cascio, D. / Eisenberg, D.
CitationJournal: 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
DepositionDec 11, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 12, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Alpha-crystallin B chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,1153
Polymers10,9231
Non-polymers1922
Water0
1
A: Alpha-crystallin B chain
hetero molecules

A: Alpha-crystallin B chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,2316
Polymers21,8472
Non-polymers3844
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555-y,-x,-z+1/31
Buried area2610 Å2
ΔGint-13 kcal/mol
Surface area11840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.950, 50.950, 104.430
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number153
Space group name H-MP3212

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Components

#1: Protein Alpha-crystallin B chain / CRYAB / Alpha(B)-crystallin / Rosenthal fiber component / Heat shock protein beta-5 / HspB5 / Renal ...Alpha(B)-crystallin / Rosenthal fiber component / Heat shock protein beta-5 / HspB5 / Renal carcinoma antigen NY-REN-27


Mass: 10923.354 Da / Num. of mol.: 1 / Fragment: residues 68-162
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CRYA2, CRYAB / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P02511
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.6 Å3/Da / Density % sol: 65.84 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 0.08M SODIUM ACETATE pH 4.6, 20% GLYCEROL, 1.8M AMMONIUM SULFATE, vapor diffusion, sitting drop, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 1.49 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 15, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.49 Å / Relative weight: 1
ReflectionResolution: 3.15→18.88 Å / Num. obs: 2777 / % possible obs: 98.3 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 93.901 Å2 / Rmerge(I) obs: 0.055 / Net I/σ(I): 19.05
Reflection shell
Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
3.15-3.230.5293.2121320798.6
3.23-3.320.5153.71159192100
3.32-3.420.2885.71180203100
3.42-3.520.1838.9109318099.4
3.52-3.640.14111.1107819398.5
3.64-3.770.11111.9101016499.4
3.77-3.910.09814.31036174100
3.91-4.070.07719.5944160100
4.07-4.250.0622.291016397.6
4.25-4.460.04427.8880144100
4.46-4.70.04828.387115098.7
4.7-4.980.03831.9777136100
4.98-5.330.04329.1714127100
5.33-5.750.0430.266512099.2
5.75-6.30.04831.266611695.9
6.3-7.040.05130.65079698
7.04-8.130.03635.85299496.9
8.13-9.960.03635.44067798.7
9.96-14.090.03136.13156196.8
14.090.03835.1962051.3

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASERphasing
PHENIX1.4_4refinement
PDB_EXTRACT3.005data extraction
ADSCQuantumdata collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.32→18.878 Å / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.669 / SU ML: -0 / σ(F): 1.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.327 238 10.02 %
Rwork0.299 --
obs0.301 2376 98.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 148.701 Å2 / ksol: 0.301 e/Å3
Displacement parametersBiso max: 345.5 Å2 / Biso mean: 165.659 Å2 / Biso min: 20 Å2
Baniso -1Baniso -2Baniso -3
1--5.55 Å2-0 Å2-0 Å2
2---5.55 Å20 Å2
3----42.263 Å2
Refinement stepCycle: LAST / Resolution: 3.32→18.878 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms749 0 10 0 759
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007771
X-RAY DIFFRACTIONf_angle_d1.2181043
X-RAY DIFFRACTIONf_chiral_restr0.08116
X-RAY DIFFRACTIONf_plane_restr0.006137
X-RAY DIFFRACTIONf_dihedral_angle_d20.663294
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 2

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.32-4.1760.3981180.3851058117699
4.176-18.8780.3021200.2651080120098
Refinement TLS params.Method: refined / Origin x: 13.9412 Å / Origin y: -6.1514 Å / Origin z: 3.5444 Å
111213212223313233
T0.9859 Å20.4661 Å20.0688 Å2-0.658 Å2-0.1331 Å2--0.606 Å2
L2.233 °2-0.3826 °2-0.2028 °2-3.7553 °2-0.9134 °2--0.7457 °2
S-0.002 Å °-0.2507 Å °-0.0501 Å °-1.426 Å °-0.8288 Å °-0.7592 Å °0.5644 Å °-0.5859 Å °0.6222 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA68 - 162
2X-RAY DIFFRACTION1allA1 - 2

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