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- PDB-3sgm: Bromoderivative-2 of amyloid-related segment of alphaB-crystallin... -

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Basic information

Entry
Database: PDB / ID: 3sgm
TitleBromoderivative-2 of amyloid-related segment of alphaB-crystallin residues 90-100
ComponentsAlpha-crystallin B chainCRYAB
KeywordsPROTEIN FIBRIL / amyloid / amyloid oligomer / beta cylindrin
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 / SAD / MAD / Resolution: 1.7006 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Alpha-crystallin B chain
B: Alpha-crystallin B chain
C: Alpha-crystallin B chain
D: Alpha-crystallin B chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,2285
Polymers5,1094
Non-polymers1181
Water28816
1
A: Alpha-crystallin B chain
B: Alpha-crystallin B chain
hetero molecules

A: Alpha-crystallin B chain
B: Alpha-crystallin B chain
hetero molecules

A: Alpha-crystallin B chain
B: Alpha-crystallin B chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,0199
Polymers7,6646
Non-polymers3553
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area5870 Å2
ΔGint-30 kcal/mol
Surface area4230 Å2
MethodPISA
2
C: Alpha-crystallin B chain
D: Alpha-crystallin B chain

C: Alpha-crystallin B chain
D: Alpha-crystallin B chain

C: Alpha-crystallin B chain
D: Alpha-crystallin B chain


Theoretical massNumber of molelcules
Total (without water)7,6646
Polymers7,6646
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area6530 Å2
ΔGint-51 kcal/mol
Surface area4480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.995, 65.995, 65.995
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number199
Space group name H-MI213

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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: 1277.348 Da / Num. of mol.: 4 / Source method: obtained synthetically / Details: synthetic peptide / Source: (synth.) Homo sapiens (human) / References: UniProt: P02511
#2: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 16 / 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: 2.34 Å3/Da / Density % sol: 47.52 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.1M TRIS pH 7.0, 35% MPD, 0.2M SODIUM CHLORIDE, vapor diffusion, hanging drop, temperature 298K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONALS 8.2.210.92
SYNCHROTRONALS 8.2.221
Detector
TypeIDDetectorDate
ADSC QUANTUM 3151CCDJan 27, 2009
ADSC QUANTUM 3152CCDJan 27, 2009
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.921
211
ReflectionResolution: 1.62→50 Å / Num. obs: 6043 / % possible obs: 97.2 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.033 / Χ2: 1.004 / Net I/σ(I): 28.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.62-1.683.70.2866131.0081,298.7
1.68-1.753.70.1885781.011,297.5
1.75-1.823.80.1316131.0061,298.6
1.82-1.923.80.0915961.0031,297.9
1.92-2.043.70.0616191.0051,299.2
2.04-2.23.70.0516051.0051,298.2
2.2-2.423.60.0415900.9971,296.9
2.42-2.773.40.0316001.0031,296.6
2.77-3.493.20.0236020.9991,294.7
3.49-503.40.01762711,294.1

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SHELXphasing
DMphasing
PHENIX1.7.1_743refinement
PDB_EXTRACT3.1data extraction
SHELXDphasing
RefinementMethod to determine structure: SAD / Resolution: 1.7006→32.998 Å / Occupancy max: 1 / Occupancy min: 0.35 / FOM work R set: 0.8159 / SU ML: 0.32 / σ(F): 1.41 / Phase error: 24.29 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2397 257 4.75 %
Rwork0.1922 --
obs0.1944 5409 99.98 %
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60.966 Å2 / ksol: 0.43 e/Å3
Displacement parametersBiso max: 43.96 Å2 / Biso mean: 21.8548 Å2 / Biso min: 10.47 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.7006→32.998 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms340 0 8 16 364
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014361
X-RAY DIFFRACTIONf_angle_d1.796488
X-RAY DIFFRACTIONf_chiral_restr0.09265
X-RAY DIFFRACTIONf_plane_restr0.00461
X-RAY DIFFRACTIONf_dihedral_angle_d16.558146
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 2 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.7006-2.14250.20621400.137825332673
2.1425-33.00370.25431170.211926192736

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