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- PDB-6c3f: AMYLOID FORMING PEPTIDE IYKVEI FROM TRANSTHYRETIN -

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Basic information

Entry
Database: PDB / ID: 6c3f
TitleAMYLOID FORMING PEPTIDE IYKVEI FROM TRANSTHYRETIN
ComponentsILE-TYR-LYS-VAL-GLU-ILE
KeywordsPROTEIN FIBRIL / amyloid / transthyretin / fibril
Function / homologytrifluoroacetic acid
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.499 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: ILE-TYR-LYS-VAL-GLU-ILE
B: ILE-TYR-LYS-VAL-GLU-ILE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,6443
Polymers1,5302
Non-polymers1141
Water724
1
A: ILE-TYR-LYS-VAL-GLU-ILE
B: ILE-TYR-LYS-VAL-GLU-ILE
hetero molecules
x 10


Theoretical massNumber of molelcules
Total (without water)16,43930
Polymers15,29920
Non-polymers1,14010
Water36020
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_455x-1,y,z1
crystal symmetry operation1_655x+1,y,z1
crystal symmetry operation1_355x-2,y,z1
crystal symmetry operation1_755x+2,y,z1
crystal symmetry operation1_556x,y,z+11
crystal symmetry operation1_456x-1,y,z+11
crystal symmetry operation1_656x+1,y,z+11
crystal symmetry operation1_356x-2,y,z+11
crystal symmetry operation1_756x+2,y,z+11
Unit cell
Length a, b, c (Å)9.600, 29.450, 16.030
Angle α, β, γ (deg.)90.000, 95.660, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein/peptide ILE-TYR-LYS-VAL-GLU-ILE


Mass: 764.929 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#2: Chemical ChemComp-TFA / trifluoroacetic acid


Mass: 114.023 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2HF3O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / 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: 1.47 Å3/Da / Density % sol: 16.55 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 1.5 M NaCl, 10 % v/v ethanol, 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: Feb 28, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.499→15.952 Å / Num. obs: 1413 / % possible obs: 96.3 % / Redundancy: 2.735 % / Biso Wilson estimate: 5.02 Å2 / CC1/2: 0.989 / Rmerge(I) obs: 0.154 / Rrim(I) all: 0.188 / Χ2: 0.974 / Net I/σ(I): 5.06
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.5-1.562.6760.5172.081450.7650.63496.7
1.56-1.622.7870.3572.931550.8710.43895.1
1.62-1.692.7090.4562.611100.80.55795.7
1.69-1.772.7820.392.771420.8580.47597.3
1.77-1.872.6980.3163.331260.9190.3997.7
1.87-1.982.7220.2084.571260.9310.25497.7
1.98-2.122.750.1686.29960.9560.20599
2.12-2.292.7480.1576.381150.9590.19298.3
2.29-2.512.7080.1436.65960.9850.17499
2.51-2.82.8610.0997.84790.9950.12492.9
2.8-3.242.7050.0918.64880.990.10996.7
3.24-3.972.6380.0710.47580.9920.08693.5
3.97-5.612.750.06710.83520.9930.08296.3
5.61-15.9522.760.0787.94250.9980.09678.1

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIXdev_1555refinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.499→15.952 Å / SU ML: 0.11 / Cross valid method: THROUGHOUT / σ(F): 1.39 / Phase error: 28.86
RfactorNum. reflection% reflection
Rfree0.2624 141 10.07 %
Rwork0.205 --
obs0.2109 1400 96.02 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 17.89 Å2 / Biso mean: 8.12 Å2 / Biso min: 2.21 Å2
Refinement stepCycle: final / Resolution: 1.499→15.952 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms108 0 7 4 119
Biso mean--14.31 14.63 -
Num. residues----12
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008114
X-RAY DIFFRACTIONf_angle_d1.144153
X-RAY DIFFRACTIONf_chiral_restr0.04818
X-RAY DIFFRACTIONf_plane_restr0.00417
X-RAY DIFFRACTIONf_dihedral_angle_d15.55443
LS refinement shellResolution: 1.4991→1.553 Å / Rfactor Rfree error: 0 / Total num. of bins used: 1
RfactorNum. reflection% reflection
Rfree0.2423 -10 %
Rwork0.3093 --
obs-133 95 %

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