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- PDB-4xfo: Structure of an amyloid-forming segment TAVVTN from human Transth... -

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Basic information

Entry
Database: PDB / ID: 4xfo
TitleStructure of an amyloid-forming segment TAVVTN from human Transthyretin
ComponentsAmyloid-forming peptide TAVVTN
KeywordsPROTEIN FIBRIL / amyloid / transthyretin / fibril
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.35 Å
AuthorsSaelices, L. / Sawaya, M. / Cascio, D. / Eisenberg, D.S.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Marie 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 TAVVTN


Theoretical massNumber of molelcules
Total (without water)6041
Polymers6041
Non-polymers00
Water00
1
A: Amyloid-forming peptide TAVVTN

A: Amyloid-forming peptide TAVVTN

A: Amyloid-forming peptide TAVVTN

A: Amyloid-forming peptide TAVVTN


Theoretical massNumber of molelcules
Total (without water)2,4154
Polymers2,4154
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_655x+1,y,z1
crystal symmetry operation1_755x+2,y,z1
crystal symmetry operation1_855x+3,y,z1
Unit cell
Length a, b, c (Å)4.750, 10.660, 16.390
Angle α, β, γ (deg.)77.64, 87.81, 77.61
Int Tables number1
Space group name H-MP1
DetailsThe biological assembly is a pair of indefinitely long beta sheets constructed from chain A and unit cell translations along the "a" direction (that is, the "a" direction corresponds to the fiber axis) (i.e. X,Y,Z; X+1,Y,Z; X+2,Y,Z; etc.) together with a complementary sheet formed from X,Y+1,Z and its unit cell translations along the "a" direction (i.e. X+1,Y+1,Z; X+2,Y+1,Z; X+3,Y+1,Z;, etc.)

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Components

#1: Protein/peptide Amyloid-forming peptide TAVVTN


Mass: 603.665 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: This sequence corresponds to a segment from human Transthyretin
Source: (synth.) synthetic construct (others)

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 1.35 Å3/Da / Density % sol: 6.22 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.2 M Ammonium sulfate, 0.1 M BIS-TRIS pH 5.5, 25% w/v Polyethylene glycol 3,350, 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: Dec 9, 2012
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.35→16.01 Å / Num. obs: 629 / % possible obs: 92.6 % / Redundancy: 21.8 % / Net I/σ(I): 6.93

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementResolution: 1.35→16.01 Å / SU ML: 0.06 / Cross valid method: FREE R-VALUE / σ(F): 2.12 / Phase error: 13.92 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1478 63 10.1 %
Rwork0.1336 --
obs0.135 624 91.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.35→16.01 Å /
ProteinNucleic acidLigandSolventTotal
Num. atoms42 0 0 0 42
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00941
X-RAY DIFFRACTIONf_angle_d1.2757
X-RAY DIFFRACTIONf_dihedral_angle_d12.58412
X-RAY DIFFRACTIONf_chiral_restr0.05210
X-RAY DIFFRACTIONf_plane_restr0.0047

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