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- PDB-7k3y: GGYAGAS segment 52-58 from Keratin-8 -

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Basic information

Entry
Database: PDB / ID: 7k3y
TitleGGYAGAS segment 52-58 from Keratin-8
ComponentsGGYAGAS segment 52-58 from the low complexity domain of Keratin-8
KeywordsPROTEIN FIBRIL / amyloid filament / low complexity sequence
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.1 Å
AuthorsMurray, K.A. / Sawaya, M.R. / Eisenberg, D.S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P30 GM124165 United States
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2022
Title: Identifying amyloid-related diseases by mapping mutations in low-complexity protein domains to pathologies.
Authors: Murray, K.A. / Hughes, M.P. / Hu, C.J. / Sawaya, M.R. / Salwinski, L. / Pan, H. / French, S.W. / Seidler, P.M. / Eisenberg, D.S.
History
DepositionSep 14, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 10, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 1, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.year
Revision 1.2Jun 15, 2022Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title ..._citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.3Jul 6, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.4Apr 3, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

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Assembly

Deposited unit
A: GGYAGAS segment 52-58 from the low complexity domain of Keratin-8
B: GGYAGAS segment 52-58 from the low complexity domain of Keratin-8


Theoretical massNumber of molelcules
Total (without water)1,1632
Polymers1,1632
Non-polymers00
Water1267
1
A: GGYAGAS segment 52-58 from the low complexity domain of Keratin-8
B: GGYAGAS segment 52-58 from the low complexity domain of Keratin-8

A: GGYAGAS segment 52-58 from the low complexity domain of Keratin-8
B: GGYAGAS segment 52-58 from the low complexity domain of Keratin-8

A: GGYAGAS segment 52-58 from the low complexity domain of Keratin-8
B: GGYAGAS segment 52-58 from the low complexity domain of Keratin-8

A: GGYAGAS segment 52-58 from the low complexity domain of Keratin-8
B: GGYAGAS segment 52-58 from the low complexity domain of Keratin-8

A: GGYAGAS segment 52-58 from the low complexity domain of Keratin-8
B: GGYAGAS segment 52-58 from the low complexity domain of Keratin-8

A: GGYAGAS segment 52-58 from the low complexity domain of Keratin-8
B: GGYAGAS segment 52-58 from the low complexity domain of Keratin-8


Theoretical massNumber of molelcules
Total (without water)6,97912
Polymers6,97912
Non-polymers00
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_455x-1,y,z1
crystal symmetry operation1_655x+1,y,z1
crystal symmetry operation1_565x,y+1,z1
crystal symmetry operation1_465x-1,y+1,z1
crystal symmetry operation1_665x+1,y+1,z1
Unit cell
Length a, b, c (Å)9.430, 10.490, 16.630
Angle α, β, γ (deg.)88.850, 76.320, 74.060
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

#1: Protein/peptide GGYAGAS segment 52-58 from the low complexity domain of Keratin-8


Mass: 581.578 Da / Num. of mol.: 2 / Fragment: GGYAGAS / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 7 / 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: 4.5
Details: 2.5M sodium chloride, 100mM sodium acetate/acetic acid (pH 4.5), 0.2M lithium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 6, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.1→16.14 Å / Num. obs: 1830 / % possible obs: 76.2 % / Redundancy: 2.146 % / Biso Wilson estimate: 10.117 Å2 / CC1/2: 0.984 / Rmerge(I) obs: 0.157 / Rrim(I) all: 0.208 / Χ2: 0.913 / Net I/σ(I): 4.29
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.1-1.132.140.2851.86430.9510.37323.2
1.13-1.172.1650.342.08790.8950.45236.9
1.17-1.212.2390.3582.48920.8530.46651.7
1.21-1.252.1110.3362.211440.920.44486.7
1.25-1.32.180.3092.661670.8670.40389.3
1.3-1.352.10.3362.851400.7860.44882.8
1.35-1.412.2420.2923.631320.8830.38688.6
1.41-1.482.0230.2773.81310.850.37286.2
1.48-1.562.1720.2284.451340.9270.30487.6
1.56-1.652.1810.2474.711160.9370.33188.5
1.65-1.772.0480.2845.471240.750.37791.9
1.77-1.912.1270.2095.891020.8560.28382.3
1.91-2.092.1390.1886.051010.960.23990.2
2.09-2.342.2560.1346.91900.9620.17490.9
2.34-2.72.1740.1356.47860.9330.18297.7
2.7-3.32.1190.16.97670.9960.13791.8
3.3-4.672.0930.0846.77540.9630.11493.1
4.67-16.142.1430.0926.68280.9950.11893.3

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation1.2 Å16.14 Å

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Processing

Software
NameVersionClassification
PHENIX1.18.2refinement
XDS20180409data reduction
XSCALE20180409data scaling
PHASER2.8.2phasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: ideal beta strand

Resolution: 1.1→10.08 Å / SU ML: -0 / Cross valid method: FREE R-VALUE / σ(F): 2.13 / Phase error: 27.5094
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1933 181 9.99 %
Rwork0.1626 1631 -
obs0.1661 1812 75.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 9.15 Å2
Refinement stepCycle: LAST / Resolution: 1.1→10.08 Å /
ProteinNucleic acidLigandSolventTotal
Num. atoms82 0 0 7 89
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.019190
X-RAY DIFFRACTIONf_angle_d1.5167122
X-RAY DIFFRACTIONf_chiral_restr0.142110
X-RAY DIFFRACTIONf_plane_restr0.012518
X-RAY DIFFRACTIONf_dihedral_angle_d7.270328
LS refinement shellResolution: 1.1→10.08 Å
RfactorNum. reflection% reflection
Rfree0.1933 181 -
Rwork0.1626 1631 -
obs--75.5 %

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