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- PDB-6c4o: AMYLOID FORMING PEPTIDE TIAALLS FROM TRANSTHYRETIN -

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Basic information

Entry
Database: PDB / ID: 6c4o
TitleAMYLOID FORMING PEPTIDE TIAALLS FROM TRANSTHYRETIN
ComponentsTHR-ILE-ALA-ALA-LEU-LEU-SER
KeywordsPROTEIN FIBRIL / amyloid / transthyretin / fibril
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.79 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 12, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: THR-ILE-ALA-ALA-LEU-LEU-SER
B: THR-ILE-ALA-ALA-LEU-LEU-SER


Theoretical massNumber of molelcules
Total (without water)1,3762
Polymers1,3762
Non-polymers00
Water905
1
A: THR-ILE-ALA-ALA-LEU-LEU-SER
B: THR-ILE-ALA-ALA-LEU-LEU-SER
x 10


Theoretical massNumber of molelcules
Total (without water)13,75720
Polymers13,75720
Non-polymers00
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 operation2_555-x,y+1/2,-z1
crystal symmetry operation2_455-x-1,y+1/2,-z1
crystal symmetry operation2_655-x+1,y+1/2,-z1
crystal symmetry operation2_355-x-2,y+1/2,-z1
crystal symmetry operation2_255-x-3,y+1/2,-z1
Unit cell
Length a, b, c (Å)9.597, 17.306, 24.998
Angle α, β, γ (deg.)90.000, 95.760, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 687.826 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

CrystalDensity Matthews: 1.5 Å3/Da / Density % sol: 18.08 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: TIAALLS crystals were grown from 5mg/mL peptide and 10% acetonitrile. The reservoir contained 100mM Tris pH 8.5 and 0.3 M magnesium formate dihydrate. 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: Nov 8, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.79→90 Å / Num. obs: 784 / % possible obs: 97.5 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.217 / Χ2: 1.079 / Net I/σ(I): 4.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
1.8-1.942.80.5561551.002193.4
1.94-2.133.50.4291451.124199.3
2.13-2.443.70.3251591.019198.1
2.44-3.083.90.2121591.159197.5
3.08-903.70.1371661.065199.4

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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 / Resolution: 1.79→14.21 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.95 / SU B: 2.189 / SU ML: 0.07 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.204 / ESU R Free: 0.165 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2278 85 10.9 %RANDOM
Rwork0.1821 ---
obs0.1869 692 95.57 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å
Displacement parametersBiso max: 35.06 Å2 / Biso mean: 6.636 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1--0.81 Å20 Å20.2 Å2
2--0.85 Å20 Å2
3---0.01 Å2
Refinement stepCycle: final / Resolution: 1.79→14.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms96 0 0 5 101
Biso mean---27.11 -
Num. residues----14
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.02294
X-RAY DIFFRACTIONr_bond_other_d0.0010.0250
X-RAY DIFFRACTIONr_angle_refined_deg1.6412.108128
X-RAY DIFFRACTIONr_angle_other_deg0.8583130
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.111512
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.2641516
X-RAY DIFFRACTIONr_chiral_restr0.0860.222
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0292
X-RAY DIFFRACTIONr_gen_planes_other00.0212
LS refinement shellResolution: 1.794→1.839 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.76 5 -
Rwork0.187 43 -
all-48 -
obs--72.73 %

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