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- PDB-3l1e: Bovine AlphaA crystallin Zinc Bound -

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Basic information

Entry
Database: PDB / ID: 3l1e
TitleBovine AlphaA crystallin Zinc Bound
ComponentsAlpha-crystallin A chain
KeywordsCHAPERONE / 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
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 A chain
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 1.15 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 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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 A chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,0743
Polymers11,9161
Non-polymers1582
Water1,69394
1
A: Alpha-crystallin A chain
hetero molecules

A: Alpha-crystallin A chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,1476
Polymers23,8322
Non-polymers3154
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area1980 Å2
ΔGint-10 kcal/mol
Surface area14000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.215, 56.215, 68.657
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Alpha-crystallin A chain / Alpha-crystallin A chain / short form


Mass: 11916.200 Da / Num. of mol.: 1 / Fragment: residues 59-163
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
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 94 / Source method: isolated from a natural source / Formula: H2O

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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: 2.29 Å3/Da / Density % sol: 46.21 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.1M HEPES pH 7.0, 5% TACSIMATE pH 7.0, 10% PEG 5000 MME, vapor diffusion, hanging drop, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 12, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionRedundancy: 7.6 % / Av σ(I) over netI: 23.16 / Number: 135178 / Rmerge(I) obs: 0.048 / Χ2: 1.03 / D res high: 1.5 Å / D res low: 80 Å / Num. obs: 17697 / % possible obs: 96.9
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
3.238090.310.0240.9016.1
2.563.239910.030.9636.6
2.242.5699.910.0381.0227.4
2.042.2499.910.0451.0897.8
1.892.0410010.0551.0178.3
1.781.8910010.0911.0789
1.691.7810010.1281.0389.7
1.621.6999.710.181.0279.5
1.551.6294.810.2391.0766.7
1.51.5586.110.3051.0575
ReflectionResolution: 1.1→80 Å / Num. obs: 41444 / % possible obs: 91.3 % / Redundancy: 5.9 % / Rmerge(I) obs: 0.058 / Χ2: 1.046 / Net I/σ(I): 17
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.1-1.145.80.4934461.04177.3
1.14-1.186.40.4241121.09492.1
1.18-1.246.50.31641201.06292.9
1.24-1.36.50.22542051.09593.3
1.3-1.396.40.17842051.06194.1
1.39-1.496.40.12142721.08894.9
1.49-1.646.20.07843401.02295.8
1.64-1.885.70.0543861.01896.4
1.88-2.374.90.0344650.98596.9
2.37-804.30.02338930.91380.2

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Phasing

PhasingMethod: SIRAS

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SHELXphasing
PHENIX1.5_2refinement
PDB_EXTRACT3.005data extraction
ADSCQuantumdata collection
SHELXDphasing
RefinementMethod to determine structure: SIRAS / Resolution: 1.15→21.748 Å / Occupancy max: 1 / Occupancy min: 0.42 / FOM work R set: 0.928 / SU ML: 0.12 / σ(F): 0.04 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.193 1946 5.39 %
Rwork0.164 --
obs0.166 36118 90.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 57.401 Å2 / ksol: 0.466 e/Å3
Displacement parametersBiso max: 38.12 Å2 / Biso mean: 13.544 Å2 / Biso min: 5.36 Å2
Baniso -1Baniso -2Baniso -3
1--0.131 Å2-0 Å20 Å2
2---0.131 Å20 Å2
3---0.262 Å2
Refine analyzeLuzzati sigma a obs: 0.12 Å
Refinement stepCycle: LAST / Resolution: 1.15→21.748 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms835 0 7 94 936
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007927
X-RAY DIFFRACTIONf_angle_d1.2271266
X-RAY DIFFRACTIONf_chiral_restr0.093135
X-RAY DIFFRACTIONf_plane_restr0.005172
X-RAY DIFFRACTIONf_dihedral_angle_d15.367369
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.15-1.1790.1621250.1532258238386
1.179-1.2110.1491300.142300243087
1.211-1.2460.1571340.1272369250389
1.246-1.2860.1431350.122357249290
1.286-1.3320.1461390.1192423256292
1.332-1.3860.1281380.1132438257692
1.386-1.4490.1671390.1152460259992
1.449-1.5250.1421440.1172511265594
1.525-1.6210.1351440.1252527267195
1.621-1.7460.1591480.1382565271396
1.746-1.9210.1871470.1522594274196
1.921-2.1990.1781520.1552635278797
2.199-2.770.2011520.1842659281196
2.77-21.7510.3081190.2322076219571

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