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- PDB-8t84: Racemic mixture of amyloid beta segment 35-MVGGVV-40 forms hetero... -

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Open data

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Basic information

Entry

Database: PDB / ID: 8t84

Title

Racemic mixture of amyloid beta segment 35-MVGGVV-40 forms heterochiral rippled beta-sheet, includes hexafluoroisopropanol

Components

Racemic mixture of amyloid beta segment 35-MVGGVV-40

Keywords

PROTEIN FIBRIL / Rippled beta sheet / amyloid fibril

Function / homology

1,1,1,3,3,3-hexafluoropropan-2-ol

Function and homology information

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON / AB INITIO PHASING / Resolution: 1.101 Å

Authors

Sawaya, M.R. / Raskatov, J.A. / Hazari, A.

Funding support

United States, 1items

Citation

Journal: J.Am.Chem.Soc. / Year: 2023
Title: Racemic Peptides from Amyloid beta and Amylin Form Rippled beta-Sheets Rather Than Pleated beta-Sheets.
Authors: Hazari, A. / Sawaya, M.R. / Sajimon, M. / Vlahakis, N. / Rodriguez, J. / Eisenberg, D. / Raskatov, J.A.

History

Deposition	Jun 21, 2023	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Nov 29, 2023	Provider: repository / Type: Initial release
Revision 1.1	Dec 13, 2023	Group: Database references / Category: citation / citation_author Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewer	Molecule: MolmilJmol/JSmol

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Downloads & links

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Download

PDBx/mmCIF format	8t84.cif.gz	15.6 KB	Display	PDBx/mmCIF format
PDB format	pdb8t84.ent.gz		Display	PDB format
PDBx/mmJSON format	8t84.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8t84_validation.pdf.gz	384 KB	Display	wwPDB validaton report
Full document	8t84_full_validation.pdf.gz	384 KB	Display
Data in XML	8t84_validation.xml.gz	2.1 KB	Display
Data in CIF	8t84_validation.cif.gz	2.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/t8/8t84 ftp://data.pdbj.org/pub/pdb/validation_reports/t8/8t84	HTTPS FTP

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Related structure data

Related structure data	8t82C 8t86C 8t89C C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#189 - Sep 2015 Amyloids similarity (1)

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Assembly

Deposited unit

AAA: Racemic mixture of amyloid beta segment 35-MVGGVV-40

hetero molecules

897 Da, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

AAA: Racemic mixture of amyloid beta segment 35-MVGGVV-40

hetero molecules

AAA: Racemic mixture of amyloid beta segment 35-MVGGVV-40

hetero molecules

AAA: Racemic mixture of amyloid beta segment 35-MVGGVV-40

hetero molecules

AAA: Racemic mixture of amyloid beta segment 35-MVGGVV-40

hetero molecules

AAA: Racemic mixture of amyloid beta segment 35-MVGGVV-40

hetero molecules

AAA: Racemic mixture of amyloid beta segment 35-MVGGVV-40

hetero molecules

defined by author
5.38 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1
crystal symmetry operation	1_655	x+1,y,z	1
crystal symmetry operation	1_455	x-1,y,z	1
crystal symmetry operation	2_556	-x,-y,-z+1	1
crystal symmetry operation	2_456	-x-1,-y,-z+1	1
crystal symmetry operation	2_656	-x+1,-y,-z+1	1

Unit cell

Length a, b, c (Å)	9.420, 11.220, 21.120
Angle α, β, γ (deg.)	96.565, 89.572, 94.951
Int Tables number	2
Space group name H-M	P-1

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Components

#1: Protein/peptide	Racemic mixture of amyloid beta segment 35-MVGGVV-40 Mass: 560.707 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#2: Chemical	ChemComp-CFH / 1,1,1,3,3,3-hexafluoropropan-2-ol Mass: 168.038 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₃H₂F₆O
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N

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Experimental details

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 1.97 Å³/Da / Density % sol: 37.57 %
Crystal grow	Temperature: 298 K / Method: batch mode / Details: hexafluoroisopropanol, water

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 24-ID-E / Wavelength: 0.97918 Å

Detector

Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 18, 2022

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.97918 Å / Relative weight: 1

Reflection

Resolution: 1.1→20.981 Å / Num. obs: 2980 / % possible obs: 85.8 % / Redundancy: 6.5 % / CC_1/2: 0.995 / R_merge(I) obs: 0.174 / R_rim(I) all: 0.186 / Net I/σ(I): 4.88

Reflection shell

Resolution (Å)	R_merge(I) obs	Num. unique obs	CC_1/2	R_rim(I) all	Diffraction-ID
1.1-1.16	1.897	224	0.627	2.09	1
1.16-1.23	1.145	357	0.889	1.242	1
1.23-1.31	1.032	397	0.878	1.107	1
1.31-1.42	0.734	424	0.945	0.786	1
1.42-1.56	0.448	385	0.931	0.48	1
1.56-1.74	0.319	326	0.989	0.34	1
1.74-2.01	0.246	298	0.974	0.264	1
2.01-2.46	0.202	258	0.99	0.216	1
2.46-3.48	0.183	203	0.918	0.197	1
3.48-20.981	0.128	108	0.998	0.136	1

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0267	refinement
XSCALE	20220110	data scaling
XDS	20220820	data reduction
SHELXD		phasing

Refinement

Method to determine structure: AB INITIO PHASING / Resolution: 1.101→20.981 Å / Cor.coef. F_o:F_c: 0.98 / Cor.coef. F_o:F_c free: 0.985 / WR_factor R_free: 0.258 / WR_factor R_work: 0.22 / SU B: 1.233 / SU ML: 0.027 / Average fsc free: 0.8922 / Average fsc work: 0.9273 / Cross valid method: FREE R-VALUE / ESU R: 0.044 / ESU R Free: 0.041
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2038	298	10 %
R_work	0.1889	2682	-
all	0.19	-	-
obs	-	2980	85.78 %

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 21.652 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-2.602 Å²	0.529 Å²	-0.52 Å²
2-	-	3.713 Å²	0.969 Å²
3-	-	-	-1.442 Å²

Refinement step

Cycle: LAST / Resolution: 1.101→20.981 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	38	0	20	2	60

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.018	0.014	70
X-RAY DIFFRACTION	r_bond_other_d	0.004	0.017	55
X-RAY DIFFRACTION	r_angle_refined_deg	1.928	1.602	102
X-RAY DIFFRACTION	r_angle_other_deg	1.424	1.64	130
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.671	5	6
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	7.704	15	9
X-RAY DIFFRACTION	r_chiral_restr	0.14	0.2	5
X-RAY DIFFRACTION	r_gen_planes_refined	0.01	0.02	47
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	5
X-RAY DIFFRACTION	r_nbd_refined	0.099	0.2	6
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.18	0.2	34
X-RAY DIFFRACTION	r_nbtor_refined	0.127	0.2	28
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.126	0.2	21
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.05	0.2	1
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.079	0.2	4
X-RAY DIFFRACTION	r_nbd_other	0.089	0.2	13
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.237	0.2	6
X-RAY DIFFRACTION	r_mcbond_it	1.81	1.649	25
X-RAY DIFFRACTION	r_mcbond_other	1.845	1.637	24
X-RAY DIFFRACTION	r_mcangle_it	1.917	2.449	29
X-RAY DIFFRACTION	r_mcangle_other	1.886	2.46	30
X-RAY DIFFRACTION	r_scbond_it	5.289	2.496	45
X-RAY DIFFRACTION	r_scbond_other	5.532	2.438	40
X-RAY DIFFRACTION	r_scangle_it	6.302	3.719	72
X-RAY DIFFRACTION	r_scangle_other	6.4	3.619	67
X-RAY DIFFRACTION	r_lrange_it	6.932	24.592	48
X-RAY DIFFRACTION	r_lrange_other	7.365	22.982	42
X-RAY DIFFRACTION	r_rigid_bond_restr	10.582	3	125

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 5

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	R_factor all	Num. reflection all	Fsc free	Fsc work	% reflection obs (%)	WR_factor R_work
1.101-1.23	0.498	58	0.371	522	0.382	989	0.82	0.844	58.6451	0.373
1.23-1.419	0.308	81	0.304	737	0.304	867	0.816	0.897	94.3483	0.303
1.419-1.737	0.268	71	0.199	639	0.207	733	0.927	0.956	96.8622	0.2
1.737-2.447	0.193	56	0.15	499	0.153	567	0.978	0.989	97.8836	0.179
2.447-20.981	0.156	32	0.17	285	0.168	318	0.989	0.984	99.6855	0.224

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