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- PDB-7k3c: SGMGGIT segment 58-64 from Keratin-8 -

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Open data

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Basic information

Entry

Database: PDB / ID: 7k3c

Title

SGMGGIT segment 58-64 from Keratin-8

Components

SGMGGIT segment 58-64 from the low complexity domain of Keratin-8

Keywords

PROTEIN FIBRIL / amyloid filament / low complexity sequence

Function / homology

ETHANOL / TRIETHYLENE GLYCOL

Function and homology information

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON / AB INITIO PHASING / Resolution: 1.1 Å

Authors

Murray, K.A. / Sawaya, M.R. / Eisenberg, D.S.

Funding support

United States, 1items

Citation

Journal: Nat.Struct.Mol.Biol. / Year: 2022
Title: Identifying amyloid-related diseases by mapping mutations in low-complexity protein domains to pathologies.
Authors: Murray, K.A. / Hughes, M.P. / Hu, C.J. / Sawaya, M.R. / Salwinski, L. / Pan, H. / French, S.W. / Seidler, P.M. / Eisenberg, D.S.

History

Deposition	Sep 11, 2020	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Nov 10, 2021	Provider: repository / Type: Initial release
Revision 1.1	Jun 1, 2022	Group: Database references / Category: citation / citation_author Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.year
Revision 1.2	Jun 15, 2022	Group: Database references / Category: citation / citation_author Item: _citation.pdbx_database_id_PubMed / _citation.title ..._citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.3	Jul 6, 2022	Group: Database references / Category: citation Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.4	May 22, 2024	Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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	7k3c.cif.gz	20.5 KB	Display	PDBx/mmCIF format
PDB format	pdb7k3c.ent.gz	12.1 KB	Display	PDB format
PDBx/mmJSON format	7k3c.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	7k3c_validation.pdf.gz	418.4 KB	Display	wwPDB validaton report
Full document	7k3c_full_validation.pdf.gz	418.4 KB	Display
Data in XML	7k3c_validation.xml.gz	2.9 KB	Display
Data in CIF	7k3c_validation.cif.gz	3.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/k3/7k3c ftp://data.pdbj.org/pub/pdb/validation_reports/k3/7k3c	HTTPS FTP

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Related structure data

Related structure data	7k3xC 7k3yC C: citing same article (ref.)
Similar structure data	1bj6-d 1cn2-d 1na3-1 1ccv-d 3gt9-1 4oxc-4 1chv-d 2n69-d 6cfn-2 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) 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	#13 - Jan 2001 Alcohol Dehydrogenase similarity (1) #191 - Nov 2015 Glutamate-gated Chloride Receptors similarity (1) #233 - May 2019 S-Nitrosylated Hemoglobin similarity (1) #44 - Aug 2003 Calmodulin similarity (1) #241 - Jan 2020 Twenty Years of Molecules similarity (1)

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Assembly

Deposited unit

A: SGMGGIT segment 58-64 from the low complexity domain of Keratin-8

B: SGMGGIT segment 58-64 from the low complexity domain of Keratin-8

hetero molecules

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

1

A: SGMGGIT segment 58-64 from the low complexity domain of Keratin-8

B: SGMGGIT segment 58-64 from the low complexity domain of Keratin-8

hetero molecules

A: SGMGGIT segment 58-64 from the low complexity domain of Keratin-8

B: SGMGGIT segment 58-64 from the low complexity domain of Keratin-8

hetero molecules

A: SGMGGIT segment 58-64 from the low complexity domain of Keratin-8

B: SGMGGIT segment 58-64 from the low complexity domain of Keratin-8

hetero molecules

A: SGMGGIT segment 58-64 from the low complexity domain of Keratin-8

B: SGMGGIT segment 58-64 from the low complexity domain of Keratin-8

hetero molecules

A: SGMGGIT segment 58-64 from the low complexity domain of Keratin-8

B: SGMGGIT segment 58-64 from the low complexity domain of Keratin-8

hetero molecules

A: SGMGGIT segment 58-64 from the low complexity domain of Keratin-8

B: SGMGGIT segment 58-64 from the low complexity domain of Keratin-8

hetero molecules

defined by author
8.91 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	1_554	x,y,z-1	1
crystal symmetry operation	1_556	x,y,z+1	1
crystal symmetry operation	1_455	x-1,y,z	1
crystal symmetry operation	1_454	x-1,y,z-1	1
crystal symmetry operation	1_456	x-1,y,z+1	1

Unit cell

Length a, b, c (Å)	8.360, 51.610, 9.530
Angle α, β, γ (deg.)	90.000, 109.096, 90.000
Int Tables number	4
Space group name H-M	P12₁1

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Components

#1: Protein/peptide	SGMGGIT segment 58-64 from the low complexity domain of Keratin-8 Mass: 621.706 Da / Num. of mol.: 2 / Fragment: SGMGGIT / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#2: Chemical	ChemComp-EOH / ETHANOL Mass: 46.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂H₆O
#3: Chemical	ChemComp-PGE / TRIETHYLENE GLYCOL Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₆H₁₄O₄
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 5 / 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: 1.56 Å³/Da / Density % sol: 21.28 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.2 Details: 0.1 M phoshate/citrate pH 4.2, 40% ethanol, 5% PEG 1000

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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: Aug 9, 2018

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→25.81 Å / Num. obs: 2926 / % possible obs: 93.3 % / Redundancy: 2.636 % / B_iso Wilson estimate: 10.188 Å² / CC_1/2: 0.955 / R_merge(I) obs: 0.182 / R_rim(I) all: 0.224 / Χ²: 0.791 / Net I/σ(I): 3.33

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
1.1-1.13	2.007	0.351	1.39	148	0.946	0.462	62.7
1.13-1.16	2.098	0.318	1.62	164	0.932	0.406	72.6
1.16-1.19	2.408	0.299	2.08	228	0.927	0.381	93.1
1.19-1.23	2.528	0.305	2.17	193	0.895	0.383	99.5
1.23-1.27	2.47	0.308	2.11	185	0.889	0.388	100
1.27-1.31	2.687	0.29	2.25	214	0.938	0.361	100
1.31-1.36	2.67	0.276	2.73	197	0.903	0.347	97
1.36-1.42	2.667	0.257	3.02	171	0.908	0.315	96.1
1.42-1.48	2.826	0.263	3.27	178	0.904	0.322	100
1.48-1.56	2.872	0.188	3.74	164	0.927	0.235	100
1.56-1.64	2.821	0.233	3.56	168	0.955	0.285	98.8
1.64-1.74	2.618	0.18	3.86	144	0.934	0.224	94.7
1.74-1.86	2.758	0.174	4.59	132	0.944	0.216	96.4
1.86-2.01	2.725	0.198	4.82	138	0.93	0.244	99.3
2.01-2.2	2.964	0.143	5.33	112	0.963	0.174	93.3
2.2-2.46	2.911	0.169	5.61	112	0.934	0.208	99.1
2.46-2.84	3	0.211	5.54	97	0.977	0.263	98
2.84-3.48	2.6	0.156	5.61	80	0.917	0.192	94.1
3.48-4.92	3.121	0.153	6.4	66	0.946	0.186	98.5
4.92-25.81	2.657	0.162	5.5	35	0.993	0.191	100

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Processing

Software

Name	Version	Classification
XDS		data reduction
XSCALE		data scaling
REFMAC	5.8.0266	refinement
PDB_EXTRACT	3.25	data extraction
SHELXD		phasing

Refinement

Method to determine structure: AB INITIO PHASING / Resolution: 1.1→25.805 Å / Cor.coef. F_o:F_c: 0.979 / Cor.coef. F_o:F_c free: 0.974 / SU B: 1.972 / SU ML: 0.039 / Cross valid method: FREE R-VALUE / ESU R: 0.045 / ESU R Free: 0.039
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.1694	293	10.014 %
R_work	0.1562	2633	-
all	0.158	-	-
obs	-	2926	93.782 %

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: 6.298 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	1.396 Å²	-0 Å²	-0.326 Å²
2-	-	-0.316 Å²	0 Å²
3-	-	-	-0.688 Å²

Refinement step

Cycle: LAST / Resolution: 1.1→25.805 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	84	0	16	5	105

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.012	0.014	95
X-RAY DIFFRACTION	r_bond_other_d	0.009	0.018	106
X-RAY DIFFRACTION	r_angle_refined_deg	1.815	1.713	116
X-RAY DIFFRACTION	r_angle_other_deg	1.613	1.647	244
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	2.65	5	12
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	6.783	15	14
X-RAY DIFFRACTION	r_chiral_restr	0.051	0.2	12
X-RAY DIFFRACTION	r_gen_planes_refined	0.004	0.02	100
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	12
X-RAY DIFFRACTION	r_nbd_refined	0.057	0.2	5
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.194	0.2	62
X-RAY DIFFRACTION	r_nbtor_refined	0.15	0.2	43
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.126	0.2	49
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.115	0.2	4
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.341	0.2	7
X-RAY DIFFRACTION	r_nbd_other	0.191	0.2	32
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.098	0.2	9
X-RAY DIFFRACTION	r_mcbond_it	0.837	0.618	54
X-RAY DIFFRACTION	r_mcbond_other	0.77	0.614	53
X-RAY DIFFRACTION	r_mcangle_it	0.76	0.939	64
X-RAY DIFFRACTION	r_mcangle_other	0.769	0.94	65
X-RAY DIFFRACTION	r_scbond_it	2.283	1.239	41
X-RAY DIFFRACTION	r_scbond_other	2.258	1.277	42
X-RAY DIFFRACTION	r_scangle_it	2.539	1.544	52
X-RAY DIFFRACTION	r_scangle_other	2.516	7.959	53
X-RAY DIFFRACTION	r_lrange_it	1.215	8.002	74
X-RAY DIFFRACTION	r_lrange_other	1.277	8.411	75
X-RAY DIFFRACTION	r_rigid_bond_restr	8.451	3	200

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

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
1.1-1.128	0.231	15	0.3	130	0.293	238	0.816	0.784	60.9244	0.29
1.128-1.159	0.357	16	0.26	149	0.27	225	0.827	0.848	73.3333	0.274
1.159-1.193	0.237	23	0.201	206	0.205	238	0.876	0.899	96.2185	0.21
1.193-1.229	0.254	19	0.193	172	0.2	191	0.864	0.909	100	0.205
1.229-1.27	0.266	19	0.243	167	0.246	186	0.838	0.881	100	0.244
1.27-1.314	0.284	21	0.206	194	0.215	217	0.873	0.907	99.0783	0.205
1.314-1.364	0.179	20	0.171	175	0.172	197	0.927	0.937	98.9848	0.185
1.364-1.419	0.162	17	0.164	153	0.163	173	0.966	0.936	98.2659	0.173
1.419-1.482	0.2	17	0.191	161	0.192	178	0.955	0.933	100	0.2
1.482-1.554	0.172	17	0.165	145	0.166	164	0.936	0.953	98.7805	0.186
1.554-1.638	0.295	17	0.162	156	0.174	175	0.913	0.949	98.8571	0.179
1.638-1.737	0.195	14	0.165	129	0.169	145	0.946	0.947	98.6207	0.174
1.737-1.856	0.15	13	0.132	118	0.133	137	0.956	0.967	95.6204	0.149
1.856-2.004	0.114	14	0.125	125	0.124	143	0.976	0.975	97.2028	0.138
2.004-2.194	0.164	11	0.123	100	0.127	113	0.974	0.98	98.2301	0.14
2.194-2.45	0.085	11	0.129	100	0.124	113	0.987	0.978	98.2301	0.142
2.45-2.825	0.095	10	0.143	88	0.136	99	0.98	0.974	98.9899	0.173
2.825-3.45	0.13	8	0.125	73	0.125	84	0.979	0.977	96.4286	0.139
3.45-4.836	0.111	7	0.093	60	0.095	68	0.98	0.988	98.5294	0.141
4.836-25.805	0.188	4	0.187	31	0.187	35	0.893	0.973	100	0.209

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