PDB-7rol: Amyloid-related segment of alphaB-crystallin residues 90-100 with...

ID or keywords:

Entry

Database: PDB / ID: 7rol

Title

Amyloid-related segment of alphaB-crystallin residues 90-100 with G95W mutation, bromo derivative

Components

Alpha-crystallin B chain peptide

Keywords

PROTEIN FIBRIL / amyloid oligomer

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MAD / Resolution: 1.996 Å

Model details

Amyloid Oligomer

Authors

Sawaya, M.R. / Do, T.D. / Eisenberg, D.S.

Funding support

United States, 1items

Citation

Journal: Protein Sci. / Year: 2022
Title: Atomic view of an amyloid dodecamer exhibiting selective cellular toxic vulnerability in acute brain slices.
Authors: Gray, A.L.H. / Sawaya, M.R. / Acharyya, D. / Lou, J. / Edington, E.M. / Best, M.D. / Prosser, R.A. / Eisenberg, D.S. / Do, T.D.

History

Deposition	Jul 30, 2021	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Feb 16, 2022	Provider: repository / Type: Initial release
Revision 1.1	Mar 2, 2022	Group: Database references / Category: citation Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	7rol.cif.gz	14.8 KB	Display	PDBx/mmCIF format
PDB format	pdb7rol.ent.gz	9 KB	Display	PDB format
PDBx/mmJSON format	7rol.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ro/7rol ftp://data.pdbj.org/pub/pdb/validation_reports/ro/7rol	HTTPS FTP

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Related structure data

Related structure data	7rojC C: citing same article (ref.)
Similar structure data	5a0r-2 6si3-2 5a0x-1 6r51-2 4e1m-d 6r4z-1 2zlb-d 2bdi-12 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details)

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Alpha-crystallin B chain peptide

B: Alpha-crystallin B chain peptide

2.78 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Alpha-crystallin B chain peptide

B: Alpha-crystallin B chain peptide

x 6

defined by author
Evidence: mass spectrometry
16.7 kDa, 12 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	2_554	-y,x-y,z-2/3	1
crystal symmetry operation	3_554	-x+y,-x,z-1/3	1
crystal symmetry operation	4_555	-x,-y,z	1
crystal symmetry operation	5_555	y,-x+y,z+1/3	1
crystal symmetry operation	6_554	x-y,x,z-1/3	1

Unit cell

Length a, b, c (Å)	36.930, 36.930, 24.900
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	172
Space group name H-M	P6₄

#1: Protein/peptide	Alpha-crystallin B chain peptide Mass: 1392.479 Da / Num. of mol.: 2 / Fragment: residues 90-100 / Mutation: G95W / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
Has ligand of interest	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: 1.76 Å³/Da / Density % sol: 30.11 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: diammonium phosphate, methyl-2,4-pentandiol

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 24-ID-C / Wavelength: 0.92004 Å

Detector

Type: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Oct 15, 2020

Radiation

Monochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.92004 Å / Relative weight: 1

Reflection twin

Type	Crystal-ID	ID	Operator	Domain-ID	Fraction
pseudo-merohedral	1	1	H, K, L	1	0.5155
pseudo-merohedral	2	2	-K, -H, -L	2	0.4845

Reflection

Resolution: 1.996→31.982 Å / Num. obs: 1372 / % possible obs: 99.7 % / Redundancy: 19.594 % / B_iso Wilson estimate: 52.814 Å² / CC_1/2: 0.999 / R_merge(I) obs: 0.097 / R_rim(I) all: 0.1 / Χ²: 0.841 / Net I/σ(I): 14.9

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. unique obs	CC_1/2	R_rim(I) all	% possible all
2-2.07	19.067	1.794	1.61	149	0.657	1.843	100
2.07-2.16	20.756	1.56	2.24	131	0.773	1.599	99.2
2.16-2.25	19.733	0.969	4.06	131	0.957	0.994	98.5
2.25-2.36	18.709	0.999	3.41	127	0.899	1.028	99.2
2.36-2.49	19.681	0.727	4.75	119	0.982	0.747	100
2.49-2.64	20.765	0.517	6.7	115	0.975	0.53	100
2.64-2.82	20.075	0.326	10.95	107	0.984	0.334	100
2.82-3.05	19.875	0.171	19.35	96	0.993	0.175	100
3.05-3.34	19.143	0.104	26.76	91	0.999	0.106	100
3.34-3.74	19.161	0.078	29.52	87	0.999	0.08	100
3.74-4.31	19.903	0.077	38.47	72	0.999	0.079	100
4.31-5.28	19.925	0.053	47.11	67	1	0.054	100
5.28-7.47	17.745	0.058	43.64	51	1	0.06	100
7.47-31.982	17.034	0.046	48.85	29	1	0.048	100

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Phasing

Phasing	Method: MAD

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0267	refinement
XDS	20200131	data reduction
SCALEPACK	20200131	data scaling
MLPHARE	7.1.004	phasing
DM	7.1.004	phasing
PDB_EXTRACT	3.27	data extraction

Refinement

Method to determine structure:

MAD / Resolution: 1.996→31.982 Å / Cor.coef. F_o:F_c: 0.934 / Cor.coef. F_o:F_c free: 0.914 / WR_factor R_free: 0.335 / WR_factor R_work: 0.29 / SU B: 5.999 / SU ML: 0.155 / Average fsc free: 0.8926 / Average fsc work: 0.9308 / Cross valid method: FREE R-VALUE / ESU R: 0.079 / ESU R Free: 0.057
Details: Hydrogens have been added in their riding positions. The data is merohedral twinning with twinning operator: (-k -h -l) and corresponding twinned fractions: 0.515, 0.485.

	R_factor	Num. reflection	% reflection
R_free	0.3381	142	10.357 %
R_work	0.2933	1229	-
all	0.297	-	-
obs	-	1371	99.637 %

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: 59.927 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	15.073 Å²	0 Å²	0 Å²
2-	-	15.073 Å²	0 Å²
3-	-	-	-30.146 Å²

Refinement step

Cycle: LAST / Resolution: 1.996→31.982 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	188	0	0	0	188

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.008	0.014	190
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.018	208
X-RAY DIFFRACTION	r_angle_refined_deg	1.677	1.733	252
X-RAY DIFFRACTION	r_angle_other_deg	1.007	1.751	474
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	8.632	5	16
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	20.42	26.667	6
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	16.269	15	36
X-RAY DIFFRACTION	r_chiral_restr	0.097	0.2	24
X-RAY DIFFRACTION	r_gen_planes_refined	0.008	0.02	182
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	30
X-RAY DIFFRACTION	r_nbd_refined	0.187	0.2	18
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.194	0.2	183
X-RAY DIFFRACTION	r_nbtor_refined	0.179	0.2	77
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.158	0.2	110
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.175	0.2	5
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.215	0.2	12
X-RAY DIFFRACTION	r_nbd_other	0.272	0.2	46
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.255	0.2	3
X-RAY DIFFRACTION	r_xyhbond_nbd_other	0.008	0.2	1
X-RAY DIFFRACTION	r_mcbond_it	6.53	5.657	86
X-RAY DIFFRACTION	r_mcbond_other	6.554	5.641	85
X-RAY DIFFRACTION	r_mcangle_it	9.869	8.527	98
X-RAY DIFFRACTION	r_mcangle_other	9.823	8.545	99
X-RAY DIFFRACTION	r_scbond_it	5.908	6.474	104
X-RAY DIFFRACTION	r_scbond_other	5.851	6.472	104
X-RAY DIFFRACTION	r_scangle_it	9.156	9.465	154
X-RAY DIFFRACTION	r_scangle_other	9.143	9.464	154
X-RAY DIFFRACTION	r_lrange_it	13.121	59.556	178
X-RAY DIFFRACTION	r_lrange_other	13.085	59.723	179

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
1.996-2.231	0.471	41	0.294	348	X-RAY DIFFRACTION	98.9822
2.231-2.574	0.544	31	0.414	299	X-RAY DIFFRACTION	99.6979
2.574-3.147	0.44	35	0.339	256	X-RAY DIFFRACTION	100
3.147-4.43	0.309	21	0.288	204	X-RAY DIFFRACTION	100
4.43-31.982	0.194	14	0.247	122	X-RAY DIFFRACTION	100

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