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- PDB-6c3s: AMYLOID FORMING PEPTIDE YTIAAL FROM TRANSTHYRETIN -

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Basic information

Entry
Database: PDB / ID: 6c3s
TitleAMYLOID FORMING PEPTIDE YTIAAL FROM TRANSTHYRETIN
ComponentsTYR-THR-ILE-ALA-ALA-LEU
KeywordsPROTEIN FIBRIL / amyloid / transthyretin / fibril
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.602 Å
AuthorsSievers, S.A. / Sawaya, M.R. / Saelices, L. / Eisenberg, D.S.
CitationJournal: 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.
History
DepositionJan 10, 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 1.2Mar 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
Revision 1.3Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TYR-THR-ILE-ALA-ALA-LEU


Theoretical massNumber of molelcules
Total (without water)6511
Polymers6511
Non-polymers00
Water724
1
A: TYR-THR-ILE-ALA-ALA-LEU
x 20


Theoretical massNumber of molelcules
Total (without water)13,01520
Polymers13,01520
Non-polymers00
Water36020
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_545x,y-1,z1
crystal symmetry operation1_565x,y+1,z1
crystal symmetry operation1_575x,y+2,z1
crystal symmetry operation1_535x,y-2,z1
crystal symmetry operation2_455-x-1,-y,z1
crystal symmetry operation2_465-x-1,-y+1,z1
crystal symmetry operation2_445-x-1,-y-1,z1
crystal symmetry operation2_435-x-1,-y-2,z1
crystal symmetry operation2_475-x-1,-y+2,z1
crystal symmetry operation7_454-x-1/2,y+1/2,-z-1/21
crystal symmetry operation7_444-x-1/2,y-1/2,-z-1/21
crystal symmetry operation7_464-x-1/2,y+3/2,-z-1/21
crystal symmetry operation7_434-x-1/2,y-3/2,-z-1/21
crystal symmetry operation7_474-x-1/2,y+5/2,-z-1/21
crystal symmetry operation8_444x-1/2,-y-1/2,-z-1/21
crystal symmetry operation8_454x-1/2,-y+1/2,-z-1/21
crystal symmetry operation8_434x-1/2,-y-3/2,-z-1/21
crystal symmetry operation8_464x-1/2,-y+3/2,-z-1/21
crystal symmetry operation8_424x-1/2,-y-5/2,-z-1/21
Unit cell
Length a, b, c (Å)18.746, 9.578, 44.796
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-102-

HOH

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Components

#1: Protein/peptide TYR-THR-ILE-ALA-ALA-LEU


Mass: 650.764 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#2: 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: 1.54 Å3/Da / Density % sol: 20.38 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: YTIAAL crystals were grown from a solution containing 10mg/mL peptide. The reservoir contained 100mM Bis-Tris pH 5.5 and 3 M sodium chloride. Crystals were soaked on 25% Glycerol, prior to diffraction

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID13 / Wavelength: 0.895432 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jul 13, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.895432 Å / Relative weight: 1
ReflectionResolution: 1.6→90 Å / Num. obs: 625 / % possible obs: 98.9 % / Redundancy: 5.6 % / Biso Wilson estimate: 10.22 Å2 / Rmerge(I) obs: 0.103 / Χ2: 1.006 / Net I/σ(I): 9.6 / Num. measured all: 3501
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
1.6-1.725.40.3181120.861199.1
1.72-1.95.40.1751291.1041100
1.9-2.1760.1471180.9681100
2.17-2.745.70.1041271.0641100
2.74-905.40.0681391.009195.9

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Processing

Software
NameVersionClassification
PHENIXdev_1555refinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Ideal beta strand

Resolution: 1.602→22.398 Å / SU ML: 0.08 / Cross valid method: THROUGHOUT / σ(F): 1.4 / Phase error: 28.03
RfactorNum. reflection% reflection
Rfree0.244 57 9.19 %
Rwork0.1997 --
obs0.2036 620 98.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 28.35 Å2 / Biso mean: 13.43 Å2 / Biso min: 4.56 Å2
Refinement stepCycle: final / Resolution: 1.602→22.398 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms46 0 0 4 50
Biso mean---20.99 -
Num. residues----6
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00746
X-RAY DIFFRACTIONf_angle_d0.89663
X-RAY DIFFRACTIONf_chiral_restr0.0319
X-RAY DIFFRACTIONf_plane_restr0.0037
X-RAY DIFFRACTIONf_dihedral_angle_d12.59514
LS refinement shellResolution: 1.6022→1.659 Å / Rfactor Rfree error: 0 / Total num. of bins used: 1
RfactorNum. reflection% reflection
Rfree0.1911 -14 %
Rwork0.2888 563 -
obs-60 98.36 %

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