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- PDB-5txh: Polymorphic form 2 of amyloid-beta derived peptide - IFAEDV -

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Basic information

Entry
Database: PDB / ID: 5txh
TitlePolymorphic form 2 of amyloid-beta derived peptide - IFAEDV
ComponentsIFAEDV
KeywordsDE NOVO PROTEIN / protein fibril
Function / homologyISOPROPYL ALCOHOL
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
Model detailsamyloid fibril
AuthorsSangwan, S. / Sawaya, M.R. / Eisenberg, D.
CitationJournal: Protein Sci. / Year: 2018
Title: Distal amyloid beta-protein fragments template amyloid assembly.
Authors: Do, T.D. / Sangwan, S. / de Almeida, N.E.C. / Ilitchev, A.I. / Giammona, M. / Sawaya, M.R. / Buratto, S.K. / Eisenberg, D.S. / Bowers, M.T.
History
DepositionNov 16, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 15, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 10, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Mar 6, 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: IFAEDV
B: IFAEDV
C: IFAEDV
D: IFAEDV
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,8315
Polymers2,7714
Non-polymers601
Water30617
1
B: IFAEDV
C: IFAEDV

A: IFAEDV

A: IFAEDV

D: IFAEDV
hetero molecules

D: IFAEDV
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,2778
Polymers4,1576
Non-polymers1202
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z3
crystal symmetry operation3_545-x,y-1/2,-z+1/21
crystal symmetry operation3_655-x+1,y+1/2,-z+1/21
Unit cell
Length a, b, c (Å)39.520, 9.542, 43.439
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
DetailsThe biological assembly is a pair of beta sheets with beta strands. As an example, the symmetry operators to generate a pair of sheets with 4 strands in each sheet is provided

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Components

#1: Protein/peptide
IFAEDV


Mass: 692.757 Da / Num. of mol.: 4 / Source method: obtained synthetically / Details: synthesized / Source: (synth.) Homo sapiens (human)
#2: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL / Isopropyl alcohol


Mass: 60.095 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 17 / 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: 1.48 Å3/Da / Density % sol: 16.77 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5
Details: Reservoir contained 20% PEG 4000, 0.1M Sodium Citrate pH 5.6 and 20% Isopropanol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 7, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.45→29.23 Å / Num. obs: 3593 / % possible obs: 99.8 % / Redundancy: 5.4 % / Rmerge(I) obs: 0.158 / Net I/σ(I): 8.99

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
PDB_EXTRACT3.2data extraction
XDSdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5 residue beta strand

Resolution: 1.45→29.23 Å / Cor.coef. Fo:Fc: 0.987 / Cor.coef. Fo:Fc free: 0.986 / SU B: 0.96 / SU ML: 0.036 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.063 / ESU R Free: 0.058
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1384 310 9.6 %RANDOM
Rwork0.1239 ---
obs0.1253 2936 99.14 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 36.63 Å2 / Biso mean: 7.477 Å2 / Biso min: 3.26 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2--0.04 Å2-0 Å2
3----0.02 Å2
Refinement stepCycle: final / Resolution: 1.45→29.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms196 0 4 17 217
Biso mean--30.79 24.68 -
Num. residues----24
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.02213
X-RAY DIFFRACTIONr_bond_other_d0.0030.02202
X-RAY DIFFRACTIONr_angle_refined_deg2.2031.992289
X-RAY DIFFRACTIONr_angle_other_deg0.8553464
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.451524
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.95627.14314
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.9931532
X-RAY DIFFRACTIONr_chiral_restr0.1340.235
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.02238
X-RAY DIFFRACTIONr_gen_planes_other0.0010.0242
X-RAY DIFFRACTIONr_mcbond_it0.50.48196
X-RAY DIFFRACTIONr_mcbond_other0.490.47995
X-RAY DIFFRACTIONr_mcangle_it0.7440.709114
LS refinement shellResolution: 1.45→1.488 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.283 28 -
Rwork0.175 180 -
all-208 -
obs--88.89 %

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