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- PDB-8t89: Racemic mixture of amyloid beta segment 16-KLVFFA-21 forms hetero... -

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Open data

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Basic information

Entry

Database: PDB / ID: 8t89

Title

Racemic mixture of amyloid beta segment 16-KLVFFA-21 forms heterochiral rippled beta-sheet

Components

Racemic mixture of amyloid beta segment 16-KLVFFA-21

Keywords

PROTEIN FIBRIL / Rippled beta sheet / amyloid fibril

Function / homology

trifluoroacetic acid

Function and homology information

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON / AB INITIO PHASING / Resolution: 1.5 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 22, 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	8t89.cif.gz	12.8 KB	Display	PDBx/mmCIF format
PDB format	pdb8t89.ent.gz	6.4 KB	Display	PDB format
PDBx/mmJSON format	8t89.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8t89_validation.pdf.gz	382.6 KB	Display	wwPDB validaton report
Full document	8t89_full_validation.pdf.gz	382.5 KB	Display
Data in XML	8t89_validation.xml.gz	2.2 KB	Display
Data in CIF	8t89_validation.cif.gz	2.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/t8/8t89 ftp://data.pdbj.org/pub/pdb/validation_reports/t8/8t89	HTTPS FTP

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Related structure data

Related structure data	8t82C 8t84C 8t86C 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

A: Racemic mixture of amyloid beta segment 16-KLVFFA-21

hetero molecules

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

1

A: Racemic mixture of amyloid beta segment 16-KLVFFA-21

hetero molecules

A: Racemic mixture of amyloid beta segment 16-KLVFFA-21

hetero molecules

A: Racemic mixture of amyloid beta segment 16-KLVFFA-21

hetero molecules

A: Racemic mixture of amyloid beta segment 16-KLVFFA-21

hetero molecules

A: Racemic mixture of amyloid beta segment 16-KLVFFA-21

hetero molecules

A: Racemic mixture of amyloid beta segment 16-KLVFFA-21

hetero molecules

defined by author
5.03 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_566	-x,-y+1,-z+1	1
crystal symmetry operation	2_466	-x-1,-y+1,-z+1	1
crystal symmetry operation	2_666	-x+1,-y+1,-z+1	1

Unit cell

Length a, b, c (Å)	11.690, 11.700, 18.510
Angle α, β, γ (deg.)	89.955, 91.778, 110.506
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 16-KLVFFA-21 Mass: 724.909 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#2: Chemical	ChemComp-TFA / trifluoroacetic acid Mass: 114.023 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂HF₃O₂
#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: 1.63 Å³/Da / Density % sol: 24.76 % / Description: needle-shaped
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: Mar 31, 2023

Radiation

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

Radiation wavelength

Wavelength: 0.97918 Å / Relative weight: 1

Reflection

Resolution: 1.5→18.5 Å / Num. obs: 1426 / % possible obs: 97 % / Redundancy: 6 % / CC_1/2: 0.997 / R_merge(I) obs: 0.157 / R_rim(I) all: 0.172 / Net I/σ(I): 4.49

Reflection shell

Resolution (Å)	R_merge(I) obs	Num. unique obs	CC_1/2	R_rim(I) all	Diffraction-ID
1.5-1.56	1.159	139	0.767	1.265	1
1.56-1.62	0.979	146	0.841	1.067	1
1.62-1.69	0.761	149	0.907	0.83	1
1.69-1.77	0.561	122	0.933	0.613	1
1.77-1.87	0.369	128	0.981	0.403	1
1.87-1.98	0.323	120	0.976	0.356	1
1.98-2.12	0.224	103	0.983	0.246	1
2.12-2.29	0.214	115	0.994	0.233	1
2.29-2.51	0.209	92	0.973	0.231	1
2.51-2.81	0.161	91	0.993	0.178	1
2.81-3.24	0.136	79	0.995	0.149	1
3.24-3.97	0.119	63	0.991	0.132	1
3.97-5.61	0.086	54	0.998	0.094	1
5.61-18.5	0.141	23	0.997	0.154	1

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0352	refinement
XSCALE		data scaling
XDS		data reduction
SHELXT		phasing

Refinement

Method to determine structure: AB INITIO PHASING / Resolution: 1.5→18.5 Å / Cor.coef. F_o:F_c: 0.976 / Cor.coef. F_o:F_c free: 0.97 / Cross valid method: FREE R-VALUE / ESU R: 0.086 / ESU R Free: 0.078
Details: Hydrogens have been used if present in the input file

	R_factor	Num. reflection	% reflection
R_free	0.227	143	10.028 %
R_work	0.2252	1283	-
all	0.225	-	-
obs	-	1426	97.007 %

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: 24.81 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.834 Å²	1.272 Å²	0.288 Å²
2-	-	1.116 Å²	-0.319 Å²
3-	-	-	-1.546 Å²

Refinement step

Cycle: LAST / Resolution: 1.5→18.5 Å /

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	52	0	7	2	61

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.012	0.012	59
X-RAY DIFFRACTION	r_bond_other_d	0.03	0.016	57
X-RAY DIFFRACTION	r_angle_refined_deg	1.577	1.589	79
X-RAY DIFFRACTION	r_angle_other_deg	0.511	1.566	128
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.502	5	5
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	16.043	10	9
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	14.756	10	2
X-RAY DIFFRACTION	r_chiral_restr	0.058	0.2	9
X-RAY DIFFRACTION	r_gen_planes_refined	0.01	0.02	57
X-RAY DIFFRACTION	r_gen_planes_other	0	0.02	15
X-RAY DIFFRACTION	r_nbd_refined	0.134	0.2	2
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.163	0.2	34
X-RAY DIFFRACTION	r_nbtor_refined	0.212	0.2	24
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.094	0.2	34
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.031	0.2	2
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.135	0.2	3
X-RAY DIFFRACTION	r_nbd_other	0.139	0.2	32
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.12	0.2	4
X-RAY DIFFRACTION	r_mcbond_it	2.1	1.89	23
X-RAY DIFFRACTION	r_mcbond_other	2.106	1.86	23
X-RAY DIFFRACTION	r_mcangle_it	3.266	2.772	27
X-RAY DIFFRACTION	r_mcangle_other	3.385	2.819	28
X-RAY DIFFRACTION	r_scbond_it	4.535	2.74	36
X-RAY DIFFRACTION	r_scbond_other	3.911	2.449	31
X-RAY DIFFRACTION	r_scangle_it	6.718	3.928	52
X-RAY DIFFRACTION	r_scangle_other	5.827	3.459	44
X-RAY DIFFRACTION	r_lrange_it	8.269	42.362	51
X-RAY DIFFRACTION	r_lrange_other	8.037	35.129	49

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
1.5-1.676	0.34	42	0.363	375	0.361	431	0.846	0.879	96.7517	0.333
1.676-1.932	0.281	35	0.268	313	0.269	359	0.915	0.932	96.9359	0.234
1.932-2.36	0.21	29	0.239	264	0.235	305	0.971	0.96	96.0656	0.231
2.36-3.311	0.212	23	0.209	212	0.209	238	0.981	0.978	98.7395	0.219
3.311-18.5	0.199	14	0.165	119	0.168	137	0.985	0.988	97.0803	0.248

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