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- PDB-4xfn: Structure of an Amyloid forming peptide AEVVFT from Human Transth... -

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Basic information

Entry
Database: PDB / ID: 4xfn
TitleStructure of an Amyloid forming peptide AEVVFT from Human Transthyretin
ComponentsAmyloid forming peptide AEVVFT
KeywordsPROTEIN FIBRIL / amyloid / transthyretin / fibril
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsSaelices, L. / Sawaya, M. / Cascio, D. / Eisenberg, D.S.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Marie Sklodowska-Curie Actions298559 Switzerland
CitationJournal: 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
DepositionDec 27, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 21, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 28, 2015Group: Database references
Revision 1.2Dec 9, 2015Group: Database references
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Amyloid forming peptide AEVVFT
B: Amyloid forming peptide AEVVFT


Theoretical massNumber of molelcules
Total (without water)1,3292
Polymers1,3292
Non-polymers00
Water1086
1
A: Amyloid forming peptide AEVVFT
B: Amyloid forming peptide AEVVFT

A: Amyloid forming peptide AEVVFT
B: Amyloid forming peptide AEVVFT

A: Amyloid forming peptide AEVVFT
B: Amyloid forming peptide AEVVFT

A: Amyloid forming peptide AEVVFT
B: Amyloid forming peptide AEVVFT


Theoretical massNumber of molelcules
Total (without water)5,3188
Polymers5,3188
Non-polymers00
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_565x,y+1,z1
crystal symmetry operation3_555-x,y+1/2,-z+1/21
crystal symmetry operation3_565-x,y+3/2,-z+1/21
Unit cell
Length a, b, c (Å)42.750, 9.530, 18.800
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe biological assembly is a pair of indefinitely long beta sheets. The first sheet is composed of the following symmetry mates of Chain A: x,y,z; -x,1/2+y,1/2-z; x,y+1,z; -x,3/2+y,1/2-z; x,y+2,z; etc. The complementary sheet is composed of the following symmetry mates of Chain B: x,y,z; -x,1/2+y,-1/2-z; x,y+1,z; -x,3/2+y,-1/2-z; x,y+2,z; etc

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Components

#1: Protein/peptide Amyloid forming peptide AEVVFT


Mass: 664.746 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: This sequence corresponds to a segment of human transthyretin
Source: (synth.) synthetic construct (others)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 1.44 Å3/Da / Density % sol: 14.6 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 0.4M Ammonium dihydrogen phosphate, 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: PSI PILATUS 6M / Detector: PIXEL / Date: Aug 9, 2013
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.85→14.117 Å / Num. obs: 740 / % possible obs: 93.7 % / Redundancy: 23.1 % / Net I/σ(I): 4.71

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.85→14.117 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 15.64 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2008 74 10.11 %
Rwork0.1538 --
obs0.158 732 93.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.85→14.117 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms94 0 0 6 100
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00794
X-RAY DIFFRACTIONf_angle_d1.054128
X-RAY DIFFRACTIONf_dihedral_angle_d15.02628
X-RAY DIFFRACTIONf_chiral_restr0.04518
X-RAY DIFFRACTIONf_plane_restr0.00516

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