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- PDB-6c88: STRUCTURE OF THE AMYLOID FORMING PEPTIDE VAVHVF FROM TRANSTHYRETIN -

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Basic information

Entry
Database: PDB / ID: 6c88
TitleSTRUCTURE OF THE AMYLOID FORMING PEPTIDE VAVHVF FROM TRANSTHYRETIN
ComponentsVAL-ALA-VAL-HIS-VAL-PHE
KeywordsPROTEIN FIBRIL / amyloid / transthyretin / fibril
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.851 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 24, 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: VAL-ALA-VAL-HIS-VAL-PHE
B: VAL-ALA-VAL-HIS-VAL-PHE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,4363
Polymers1,3442
Non-polymers921
Water724
1
A: VAL-ALA-VAL-HIS-VAL-PHE
B: VAL-ALA-VAL-HIS-VAL-PHE
hetero molecules
x 10


Theoretical massNumber of molelcules
Total (without water)14,35730
Polymers13,43620
Non-polymers92110
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 operation4_545x+1/2,-y-1/2,-z1
crystal symmetry operation4_445x-1/2,-y-1/2,-z1
crystal symmetry operation4_645x+3/2,-y-1/2,-z1
crystal symmetry operation4_345x-3/2,-y-1/2,-z1
crystal symmetry operation4_745x+5/2,-y-1/2,-z1
Unit cell
Length a, b, c (Å)11.529, 20.360, 36.729
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein/peptide VAL-ALA-VAL-HIS-VAL-PHE


Mass: 671.806 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#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: 1.6 Å3/Da / Density % sol: 23.32 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 10mg/ml peptide solution. Reservoir contained 0.2 M Magnesium chloride hexahydrate, 0.1 M HEPES sodium pH 7.5, 30% v/v 2-Propanol. Crystals were soaked in 25% glycerol prior to diffraction

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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 27, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.85→100 Å / Num. obs: 744 / % possible obs: 84.3 % / Redundancy: 3.8 % / Biso Wilson estimate: 4.01 Å2 / Rmerge(I) obs: 0.28 / Χ2: 1.107 / Net I/σ(I): 3.1 / Num. measured all: 2837
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
1.85-1.922.60.421711.093178.9
1.92-1.994.30.572571.238178.1
1.99-2.084.30.507661.143178.6
2.08-2.193.80.406670.934180.7
2.19-2.3340.411670.949172
2.33-2.5140.396650.997183.3
2.51-2.764.10.399811.124195.3
2.76-3.1640.382831.185192.2
3.16-3.993.70.161921.061191.1
3.99-1003.50.089951.286189.6

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHENIX1.12_2829refinement
PDB_EXTRACT3.24data extraction
DENZOdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.851→18.365 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 12.01
RfactorNum. reflection% reflection
Rfree0.1785 57 7.83 %
Rwork0.1706 --
obs0.1723 728 84.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 23.47 Å2 / Biso mean: 3.7137 Å2 / Biso min: 0.34 Å2
Refinement stepCycle: final / Resolution: 1.851→18.365 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms96 0 6 4 106
Biso mean--15.47 6.71 -
Num. residues----12
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.009103
X-RAY DIFFRACTIONf_angle_d0.827139
X-RAY DIFFRACTIONf_chiral_restr0.06718
X-RAY DIFFRACTIONf_plane_restr0.00316
X-RAY DIFFRACTIONf_dihedral_angle_d10.92752
LS refinement shellResolution: 1.8506→1.917 Å / Rfactor Rfree error: 0 / Total num. of bins used: 1
RfactorNum. reflection% reflection
Rfree0.4292 -8 %
Rwork0.1898 --
obs-70 79.55 %

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