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- PDB-3sgs: Amyloid-related segment of alphaB-crystallin residues 95-100 -

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Basic information

Entry
Database: PDB / ID: 3sgs
TitleAmyloid-related segment of alphaB-crystallin residues 95-100
ComponentsAlpha-crystallin B chainCRYAB
KeywordsPROTEIN FIBRIL / amyloid / amyloid fibril
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 / Hsp20/alpha crystallin family / Small heat shock protein (sHSP) domain profile. / Alpha crystallin/Hsp20 domain / HSP20-like chaperone
Similarity search - Domain/homology
Alpha-crystallin B chain
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.703 Å
AuthorsLaganowsky, A. / Sawaya, M.R. / Cascio, D. / Eisenberg, D.
CitationJournal: Science / Year: 2012
Title: Atomic view of a toxic amyloid small oligomer.
Authors: Laganowsky, A. / Liu, C. / Sawaya, M.R. / Whitelegge, J.P. / Park, J. / Zhao, M. / Pensalfini, A. / Soriaga, A.B. / Landau, M. / Teng, P.K. / Cascio, D. / Glabe, C. / Eisenberg, D.
History
DepositionJun 15, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 21, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Alpha-crystallin B chain


Theoretical massNumber of molelcules
Total (without water)6311
Polymers6311
Non-polymers00
Water362
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)4.821, 19.500, 21.004
Angle α, β, γ (deg.)90.000, 94.230, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 630.688 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: synthetic peptide / Source: (synth.) Homo sapiens (human) / References: UniProt: P02511
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 2 / 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

Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 2.1M DL-MALIC ACID pH 7.0, vapor diffusion, hanging drop, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 25, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.7→90 Å / Num. obs: 438 / % possible obs: 97.6 % / Redundancy: 4.9 % / Rmerge(I) obs: 0.178 / Χ2: 2.341 / Net I/σ(I): 24.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.7-1.8350.386821.8941100
1.83-2.024.80.215837.8221100
2.02-2.314.80.205990.9091100
2.31-2.915.10.155780.71191.8
2.91-904.80.146960.875196

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.703→14.27 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.875 / WRfactor Rfree: 0.2767 / WRfactor Rwork: 0.2494 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8599 / SU B: 2.719 / SU ML: 0.089 / SU R Cruickshank DPI: 0.1806 / SU Rfree: 0.1383 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.181 / ESU R Free: 0.138 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2249 43 10 %RANDOM
Rwork0.2123 ---
obs0.2133 428 97.72 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 30.6 Å2 / Biso mean: 9.9159 Å2 / Biso min: 3.89 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å20 Å2-0.01 Å2
2--0.03 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.703→14.27 Å /
ProteinNucleic acidLigandSolventTotal
Num. atoms44 0 0 2 46
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.02243
X-RAY DIFFRACTIONr_bond_other_d0.0070.0223
X-RAY DIFFRACTIONr_angle_refined_deg1.132.04758
X-RAY DIFFRACTIONr_angle_other_deg0.709359
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.28255
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.623302
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.268157
X-RAY DIFFRACTIONr_chiral_restr0.0490.28
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0247
X-RAY DIFFRACTIONr_gen_planes_other0.0010.025
X-RAY DIFFRACTIONr_mcbond_it0.9941.529
X-RAY DIFFRACTIONr_mcbond_other0.0851.512
X-RAY DIFFRACTIONr_mcangle_it1.697247
X-RAY DIFFRACTIONr_scbond_it0.751314
X-RAY DIFFRACTIONr_scangle_it1.1954.511
LS refinement shellResolution: 1.703→1.901 Å / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.201 11 -
Rwork0.292 99 -
all-110 -
obs--100 %

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