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- PDB-6c3t: AMYLOID FORMING PEPTIDE AADTWE FROM TRANSTHYRETIN WITH ATTR-D38A ... -

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Basic information

Entry
Database: PDB / ID: 6c3t
TitleAMYLOID FORMING PEPTIDE AADTWE FROM TRANSTHYRETIN WITH ATTR-D38A MUTATION ASSOCIATED WITH A FAMILIAL FORM OF TRANSTHYRETIN AMYLOIDOSIS
ComponentsALA-ALA-ASP-THR-TRP-GLU
KeywordsPROTEIN FIBRIL / amyloid / transthyretin / fibril
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1 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: ALA-ALA-ASP-THR-TRP-GLU
B: ALA-ALA-ASP-THR-TRP-GLU


Theoretical massNumber of molelcules
Total (without water)1,3832
Polymers1,3832
Non-polymers00
Water905
1
A: ALA-ALA-ASP-THR-TRP-GLU
B: ALA-ALA-ASP-THR-TRP-GLU
x 10


Theoretical massNumber of molelcules
Total (without water)13,83420
Polymers13,83420
Non-polymers00
Water36020
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_556x,y,z+11
crystal symmetry operation1_554x,y,z-11
crystal symmetry operation1_553x,y,z-21
crystal symmetry operation1_557x,y,z+21
crystal symmetry operation1_655x+1,y,z1
crystal symmetry operation1_656x+1,y,z+11
crystal symmetry operation1_654x+1,y,z-11
crystal symmetry operation1_657x+1,y,z+21
crystal symmetry operation1_653x+1,y,z-21
Unit cell
Length a, b, c (Å)9.019, 43.157, 9.392
Angle α, β, γ (deg.)90.000, 102.840, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein/peptide ALA-ALA-ASP-THR-TRP-GLU


Mass: 691.686 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 5 / 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

Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: AADTWE crystals were grown from a solution containing 100 mg/ml peptide. The reservoir contained 0.2 M Ammonium phosphate monobasic, 0.1 M Tris pH 8.5, and 50 % v/v MPD. Crystals were soaked ...Details: AADTWE crystals were grown from a solution containing 100 mg/ml peptide. The reservoir contained 0.2 M Ammonium phosphate monobasic, 0.1 M Tris pH 8.5, and 50 % v/v MPD. Crystals were soaked on 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: Oct 29, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1→90 Å / Num. obs: 3204 / % possible obs: 83.5 % / Redundancy: 13.9 % / Rmerge(I) obs: 0.128 / Χ2: 1.071 / Net I/σ(I): 11.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
1-1.0810.50.3973531.027146.8
1.08-1.1913.80.2446891.107188.9
1.19-1.3614.80.1876951.092191.7
1.36-1.7114.80.1397011.032192.5
1.71-9014.10.0897661.073196.7

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
REFMAC5.4.0061refinement
PDB_EXTRACT3.24data extraction
DENZOdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Ideal beta strand

Resolution: 1→21.58 Å / Cor.coef. Fo:Fc: 0.983 / Cor.coef. Fo:Fc free: 0.977 / SU B: 0.639 / SU ML: 0.015 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.027 / ESU R Free: 0.026 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.124 295 9.3 %RANDOM
Rwork0.1093 ---
obs0.1107 2887 82.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å
Displacement parametersBiso max: 32.14 Å2 / Biso mean: 3.311 Å2 / Biso min: 2.15 Å2
Baniso -1Baniso -2Baniso -3
1-0.87 Å20 Å20.12 Å2
2---0.5 Å20 Å2
3----0.32 Å2
Refinement stepCycle: final / Resolution: 1→21.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms98 0 0 5 103
Biso mean---13.4 -
Num. residues----12
LS refinement shellResolution: 0.996→1.022 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.177 10 -
Rwork0.203 86 -
all-96 -
obs--32.88 %

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