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- PDB-6c3g: AMYLOID FORMING PEPTIDE KALGIS FROM TRANSTHYRETIN -

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Basic information

Entry
Database: PDB / ID: 6c3g
TitleAMYLOID FORMING PEPTIDE KALGIS FROM TRANSTHYRETIN
ComponentsLYS-ALA-LEU-GLY-ILE-SER
KeywordsPROTEIN FIBRIL / amyloid / transthyretin / fibril
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.601 Å
AuthorsSaelices, L. / Sawaya, M.R. / Eisenberg, D.S.
Funding support United States, 1items
OrganizationGrant numberCountry
Seventh Framework Programme for Research298559 United States
Citation
Journal: Protein Sci. / Year: 2018
Title: Crystal structures of amyloidogenic segments of human transthyretin.
Authors: Saelices, L. / Sievers, S.A. / Sawaya, M.R. / Eisenberg, D.S.
#1: Journal: J. Biol. Chem. / Year: 2015
Title: Uncovering the Mechanism of Aggregation of Human Transthyretin.
Authors: Saelices, L. / Johnson, L.M. / Liang, W.Y. / Sawaya, M.R. / Cascio, D. / Ruchala, P. / Whitelegge, J. / Jiang, L. / Riek, R. / Eisenberg, D.S.
History
DepositionJan 9, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 18, 2018Provider: repository / Type: Initial release
Revision 1.1Jul 18, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Aug 1, 2018Group: Data collection / Database references
Category: citation / citation_author / pdbx_related_exp_data_set
Revision 1.3Mar 13, 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: LYS-ALA-LEU-GLY-ILE-SER
B: LYS-ALA-LEU-GLY-ILE-SER
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,3664
Polymers1,1772
Non-polymers1882
Water362
1
A: LYS-ALA-LEU-GLY-ILE-SER
B: LYS-ALA-LEU-GLY-ILE-SER
hetero molecules
x 10


Theoretical massNumber of molelcules
Total (without water)13,65640
Polymers11,77420
Non-polymers1,88220
Water18010
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_545x,y-1,z1
crystal symmetry operation1_565x,y+1,z1
crystal symmetry operation1_535x,y-2,z1
crystal symmetry operation1_575x,y+2,z1
crystal symmetry operation1_655x+1,y,z1
crystal symmetry operation1_665x+1,y+1,z1
crystal symmetry operation1_635x+1,y-2,z1
crystal symmetry operation1_675x+1,y+2,z1
crystal symmetry operation1_645x+1,y-1,z1
Unit cell
Length a, b, c (Å)8.060, 9.480, 25.660
Angle α, β, γ (deg.)96.940, 96.350, 110.050
Int Tables number1
Space group name H-MP1

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Components

#1: Protein/peptide LYS-ALA-LEU-GLY-ILE-SER


Mass: 588.718 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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

CrystalDensity Matthews: 1.53 Å3/Da / Density % sol: 19.71 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 3.5
Details: 0.1 M Citric acid pH 3.5, 2.0 M Ammonium sulfate, 25% Glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 1, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.6→12.566 Å / Num. obs: 871 / % possible obs: 95.6 % / Redundancy: 2.912 % / Biso Wilson estimate: 9.92 Å2 / CC1/2: 0.988 / Rmerge(I) obs: 0.138 / Rrim(I) all: 0.169 / Χ2: 1.154 / Net I/σ(I): 5.72 / Num. measured all: 2536
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.6-1.72.930.6751.411290.7650.8393.5
1.7-1.813.0230.5482.021280.6320.67195.5
1.81-1.963.0640.234.081400.9540.28194.6
1.96-2.152.8250.2114.851030.9290.25798.1
2.15-2.43.0260.1746.911140.9450.21496.6
2.4-2.772.9440.1288.08900.920.156100
2.77-3.42.6320.0889.35760.9910.10695
3.4-4.82.6090.06113.56640.9860.07695.5
4.8-12.5662.7410.03914.012710.04787.1

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIX1.8.1_1168refinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.601→12.566 Å / SU ML: 0 / Cross valid method: THROUGHOUT / σ(F): 2 / Phase error: 24.35
RfactorNum. reflection% reflection
Rfree0.2116 87 10 %
Rwork0.1812 --
obs0.1848 870 95.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 32.44 Å2 / Biso mean: 14.45 Å2 / Biso min: 5.84 Å2
Refinement stepCycle: final / Resolution: 1.601→12.566 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms82 0 11 2 95
Biso mean--27.18 26.62 -
Num. residues----12
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00689
X-RAY DIFFRACTIONf_angle_d1.17115
X-RAY DIFFRACTIONf_chiral_restr0.06914
X-RAY DIFFRACTIONf_plane_restr0.00312
X-RAY DIFFRACTIONf_dihedral_angle_d12.95732
LS refinement shellResolution: 1.6005→1.659 Å / Rfactor Rfree error: 0 / Total num. of bins used: 1
RfactorNum. reflection% reflection
Rfree0.2452 -8 %
Rwork0.2499 --
obs-70 92.11 %

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