PDB-9n31: Racemic mixture of peptide QVGGVV forms rippled sheets

ID or keywords:

Entry

Database: PDB / ID: 9n31

Title

Racemic mixture of peptide QVGGVV forms rippled sheets

Components

QVGGVV

Keywords

PROTEIN FIBRIL / rippled sheet / racemic mixture

Biological species

synthetic construct (others)

Method

X-RAY DIFFRACTION /

SYNCHROTRON / AB INITIO PHASING / Resolution: 1.102 Å

Authors

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

Funding support

United States, 3items

Organization	Grant number	Country
National Institutes of Health/National Institute on Aging (NIH/NIA)	R01AG070895	United States
National Institutes of Health/National Institute on Aging (NIH/NIA)	R01AG048120	United States
National Institutes of Health/National Institute on Aging (NIH/NIA)	R01AG074954	United States

Citation

Journal: Chem Sci / Year: 2025
Title: Formation of rippled beta-sheets from mixed chirality linear and cyclic peptides-new structural motifs based on the pauling-corey rippled beta-sheet.
Authors: Hazari, A. / Sawaya, M.R. / Lee, H. / Sajimon, M. / Kim, H. / Goddard Iii, W.A. / Eisenberg, D. / Raskatov, J.A.

History

Deposition	Jan 29, 2025	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Mar 26, 2025	Provider: repository / Type: Initial release
Revision 1.1	Apr 16, 2025	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

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9n31.cif.gz	14.9 KB	Display	PDBx/mmCIF format
PDB format	pdb9n31.ent.gz	7.4 KB	Display	PDB format
PDBx/mmJSON format	9n31.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/n3/9n31 ftp://data.pdbj.org/pub/pdb/validation_reports/n3/9n31	HTTPS FTP

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Related structure data

Related structure data	9dywC 9dyxC 9dyyC 9dyzC 9dz0C 9dz1C 9n35C C: citing same article (ref.)

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: QVGGVV

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

1

A: QVGGVV

x 6

defined by author
3.35 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_554	x,y,z-1	1
crystal symmetry operation	1_556	x,y,z+1	1
crystal symmetry operation	2_665	-x+1,-y+1,-z	1
crystal symmetry operation	2_664	-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)	23.720, 7.360, 9.240
Angle α, β, γ (deg.)	91.193, 90.619, 98.086
Int Tables number	2
Space group name H-M	P-1

#1: Protein/peptide	QVGGVV Mass: 557.640 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	N

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 1.43 Å³/Da / Density % sol: 14.08 % / Description: needle
Crystal grow	Temperature: 298 K / Method: batch mode / pH: 4 / Details: 10% isopropanol in water / PH range: 3-6

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

NSLS-II

/ Beamline: 17-ID-2 / Wavelength: 0.97933 Å

Detector

Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 11, 2024

Radiation

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

Radiation wavelength

Wavelength: 0.97933 Å / Relative weight: 1

Reflection

Resolution: 1.1→23.482 Å / Num. obs: 2243 / % possible obs: 89.4 % / Redundancy: 3.5 % / CC_1/2: 0.98 / R_merge(I) obs: 0.169 / R_rim(I) all: 0.2 / Net I/σ(I): 4.84

Reflection shell

Resolution (Å)	R_merge(I) obs	Num. unique obs	CC_1/2	R_rim(I) all	Diffraction-ID
1.1-1.13	0.39	94	0.843	0.49	1
1.13-1.16	0.381	159	0.92	0.492	1
1.16-1.2	0.276	152	0.93	0.347	1
1.2-1.23	0.592	156	0.886	0.692	1
1.23-1.27	0.563	137	0.894	0.652	1
1.27-1.32	0.389	156	0.948	0.454	1
1.32-1.37	0.264	127	0.951	0.309	1
1.37-1.42	0.421	155	0.918	0.492	1
1.42-1.49	0.331	140	0.913	0.382	1
1.49-1.56	0.299	117	0.945	0.346	1
1.56-1.64	0.205	117	0.973	0.24	1
1.64-1.74	0.204	120	0.96	0.24	1
1.74-1.86	0.172	118	0.94	0.206	1
1.86-2.01	0.168	96	0.983	0.197	1
2.01-2.2	0.126	90	0.98	0.147	1
2.2-2.46	0.133	96	0.987	0.155	1
2.46-2.85	0.139	69	0.954	0.163	1
2.85-3.48	0.128	67	0.981	0.15	1
3.48-4.93	0.127	49	0.979	0.15	1
4.93-23.482	0.1	28	0.999	0.128	1

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0419	refinement
XSCALE	VERSION Jun 30, 2024 BUILT=20240723	data scaling
XDS	VERSION Jun 30, 2024 BUILT=20240723	data reduction
SHELXT	VERSION 2018/2	phasing

Refinement

Method to determine structure: AB INITIO PHASING / Resolution: 1.102→23.482 Å / Cor.coef. F_o:F_c: 0.977 / Cor.coef. F_o:F_c free: 0.968 / SU B: 0.815 / SU ML: 0.017 / Cross valid method: FREE R-VALUE / ESU R: 0.03 / ESU R Free: 0.032
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.1844	225	10.036 %
R_work	0.1571	2017	-
all	0.16	-	-
obs	-	2242	89.394 %

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: 7.325 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.752 Å²	0.498 Å²	-0.029 Å²
2-	-	0.816 Å²	0.428 Å²
3-	-	-	-0.259 Å²

Refinement step

Cycle: LAST / Resolution: 1.102→23.482 Å /

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	39	0	0	4	43

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.011	0.011	38
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	43
X-RAY DIFFRACTION	r_angle_refined_deg	1.403	1.675	51
X-RAY DIFFRACTION	r_angle_other_deg	0.442	1.716	96
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.537	5	5
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	3.398	10	5
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	11.241	10	1
X-RAY DIFFRACTION	r_chiral_restr	0.048	0.2	7
X-RAY DIFFRACTION	r_gen_planes_refined	0.01	0.02	45
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	7
X-RAY DIFFRACTION	r_nbd_refined	0.151	0.2	6
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.173	0.2	27
X-RAY DIFFRACTION	r_nbtor_refined	0.148	0.2	20
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.093	0.2	24
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.026	0.2	2
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.069	0.2	3
X-RAY DIFFRACTION	r_nbd_other	0.192	0.2	20
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.079	0.2	6
X-RAY DIFFRACTION	r_mcbond_it	2.88	0.667	23
X-RAY DIFFRACTION	r_mcbond_other	2.879	0.664	23
X-RAY DIFFRACTION	r_mcangle_it	3.972	1.192	27
X-RAY DIFFRACTION	r_mcangle_other	3.911	1.199	28
X-RAY DIFFRACTION	r_scbond_it	3.789	0.853	15
X-RAY DIFFRACTION	r_scbond_other	3.687	0.872	16
X-RAY DIFFRACTION	r_scangle_it	5.132	1.548	24
X-RAY DIFFRACTION	r_scangle_other	5.031	1.554	25
X-RAY DIFFRACTION	r_lrange_it	5.728	9.261	41
X-RAY DIFFRACTION	r_lrange_other	5.762	7.751	40
X-RAY DIFFRACTION	r_rigid_bond_restr	3.211	3	81

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
1.102-1.232	0.28	56	0.246	502	0.25	719	0.936	0.935	77.6078	0.222
1.232-1.422	0.193	58	0.162	516	0.165	624	0.972	0.974	91.9872	0.144
1.422-1.739	0.144	49	0.139	444	0.139	528	0.986	0.981	93.3712	0.125
1.739-2.453	0.173	40	0.13	362	0.134	418	0.965	0.985	96.1722	0.134
2.453-23.482	0.17	22	0.154	193	0.156	219	0.983	0.983	98.1735	0.188

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