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- PDB-7k3x: SGMGCIT segment 58-64 from Keratin-8 with G62C mutation -

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Open data

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Basic information

Entry

Database: PDB / ID: 7k3x

Title

SGMGCIT segment 58-64 from Keratin-8 with G62C mutation

Components

SGMGCIT segment 58-64 from Keratin-8 with G62C mutation

Keywords

PROTEIN FIBRIL / amyloid filament / low complexity sequence / cryptogenic liver disease

Function / homology

ISOPROPYL ALCOHOL

Function and homology information

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 1.705 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 14, 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 / Derived calculations / Category: atom_type / citation Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.4	Apr 3, 2024	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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	7k3x.cif.gz	12.1 KB	Display	PDBx/mmCIF format
PDB format	pdb7k3x.ent.gz	5.3 KB	Display	PDB format
PDBx/mmJSON format	7k3x.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/k3/7k3x ftp://data.pdbj.org/pub/pdb/validation_reports/k3/7k3x	HTTPS FTP

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Related structure data

Related structure data	7k3cC 7k3yC C: citing same article (ref.)
Similar structure data	1pmk-2 7a3m-d 4ait-d 6tj4-1 1kiv-d 7a1h-d 4oxc-4 1coa-d 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	#70 - Oct 2005 Designer Proteins similarity (1)

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Assembly

Deposited unit

A: SGMGCIT segment 58-64 from Keratin-8 with G62C mutation

hetero molecules

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

1

A: SGMGCIT segment 58-64 from Keratin-8 with G62C mutation

hetero molecules

A: SGMGCIT segment 58-64 from Keratin-8 with G62C mutation

hetero molecules

A: SGMGCIT segment 58-64 from Keratin-8 with G62C mutation

hetero molecules

A: SGMGCIT segment 58-64 from Keratin-8 with G62C mutation

hetero molecules

A: SGMGCIT segment 58-64 from Keratin-8 with G62C mutation

hetero molecules

A: SGMGCIT segment 58-64 from Keratin-8 with G62C mutation

hetero molecules

A: SGMGCIT segment 58-64 from Keratin-8 with G62C mutation

hetero molecules

A: SGMGCIT segment 58-64 from Keratin-8 with G62C mutation

hetero molecules

A: SGMGCIT segment 58-64 from Keratin-8 with G62C mutation

hetero molecules

A: SGMGCIT segment 58-64 from Keratin-8 with G62C mutation

hetero molecules

defined by author
7.28 kDa, 10 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_455	x-1,y,z	1
crystal symmetry operation	1_655	x+1,y,z	1
crystal symmetry operation	1_355	x-2,y,z	1
crystal symmetry operation	1_755	x+2,y,z	1
crystal symmetry operation	1_556	x,y,z+1	1
crystal symmetry operation	1_456	x-1,y,z+1	1
crystal symmetry operation	1_656	x+1,y,z+1	1
crystal symmetry operation	1_356	x-2,y,z+1	1
crystal symmetry operation	1_756	x+2,y,z+1	1

Unit cell

Length a, b, c (Å)	4.740, 46.170, 10.330
Angle α, β, γ (deg.)	90.000, 103.330, 90.000
Int Tables number	4
Space group name H-M	P12₁1

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Components

#1: Protein/peptide	SGMGCIT segment 58-64 from Keratin-8 with G62C mutation Mass: 667.797 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#2: Chemical	ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL / Isopropyl alcohol Mass: 60.095 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃H₈O / Comment: alkaloid*YM
#3: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 1 / 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: 1.65 Å³/Da / Density % sol: 25.32 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.2M sodium citrate tribasic dehydrate, 0.1M HEPES (pH 7.5), 20% v/v 2-propanol

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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: 0.9791 Å

Detector

Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jun 26, 2018

Radiation

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

Radiation wavelength

Wavelength: 0.9791 Å / Relative weight: 1

Reflection twin

Type	Crystal-ID	ID	Operator	Domain-ID	Fraction
pseudo-merohedral	1	1	H, K, L	1	0.5277
pseudo-merohedral	2	2	-H, -K, H+L	2	0.4723

Reflection

Resolution: 1.7→100 Å / Num. obs: 472 / % possible obs: 93.5 % / Redundancy: 4.4 % / R_merge(I) obs: 0.192 / R_pim(I) all: 0.102 / R_rim(I) all: 0.219 / Χ²: 2.04 / Net I/σ(I): 4.3 / Num. measured all: 2087

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique obs	CC_1/2	R_pim(I) all	R_rim(I) all	Χ²	% possible all
1.7-1.76	2.6	0.947	40	0.026	0.636	1.149	1.84	71.4
1.76-1.83	3.8	0.829	32	0.567	0.433	0.937	1.492	100
1.83-1.91	3.8	0.633	51	0.408	0.371	0.739	1.629	100
1.91-2.02	3.7	0.338	46	0.783	0.199	0.395	1.465	88.5
2.02-2.14	4.5	0.325	55	0.973	0.161	0.364	2.009	93.2
2.14-2.31	6	0.297	51	0.972	0.136	0.328	1.639	100
2.31-2.54	4.8	0.241	54	0.989	0.121	0.271	1.565	98.2
2.54-2.91	4.2	0.166	32	0.974	0.124	0.21	1.535	91.4
2.91-3.66	5	0.185	55	0.98	0.094	0.208	2.722	100
3.66-100	4.8	0.123	56	0.976	0.062	0.139	3.441	94.9

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Phasing

Phasing

Method:

molecular replacement

Phasing MR

Model details: Phaser MODE: MR_AUTO

	Highest resolution	Lowest resolution
Rotation	1.71 Å	23.09 Å
Translation	1.71 Å	23.09 Å

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Processing

Software

Name	Version	Classification	NB
DENZO		data reduction
SCALEPACK		data scaling
PHASER	2.8.2	phasing
REFMAC	5.8.0266	refinement
PDB_EXTRACT	3.25	data extraction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: ideal beta strand

Resolution: 1.705→23.086 Å / Cor.coef. F_o:F_c: 0.931 / Cor.coef. F_o:F_c free: 0.924 / SU B: 4.917 / SU ML: 0.136 / Cross valid method: FREE R-VALUE / ESU R: 0.045 / ESU R Free: 0.032
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2481	45	10.045 %
R_work	0.2468	403	-
all	0.247	-	-
obs	-	448	95.117 %

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: 22.999 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-11.407 Å²	-0 Å²	-4.262 Å²
2-	-	1.134 Å²	0 Å²
3-	-	-	10.273 Å²

Refinement step

Cycle: LAST / Resolution: 1.705→23.086 Å /

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	44	0	4	1	49

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.011	0.014	46
X-RAY DIFFRACTION	r_bond_other_d	0.061	0.018	50
X-RAY DIFFRACTION	r_angle_refined_deg	1.908	1.731	59
X-RAY DIFFRACTION	r_angle_other_deg	1.593	1.646	114
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	9.503	5	6
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	17.662	15	8
X-RAY DIFFRACTION	r_chiral_restr	0.07	0.2	7
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.02	50
X-RAY DIFFRACTION	r_gen_planes_other	0	0.02	6
X-RAY DIFFRACTION	r_nbd_refined	0.083	0.2	1
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.203	0.2	25
X-RAY DIFFRACTION	r_nbtor_refined	0.137	0.2	18
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.077	0.2	28
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.243	0.2	1
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.237	0.2	7
X-RAY DIFFRACTION	r_nbd_other	0.332	0.2	20
X-RAY DIFFRACTION	r_mcbond_it	4.788	2.02	27
X-RAY DIFFRACTION	r_mcbond_other	4.858	1.984	26
X-RAY DIFFRACTION	r_mcangle_it	8.142	3.003	28
X-RAY DIFFRACTION	r_mcangle_other	8.003	3.061	29
X-RAY DIFFRACTION	r_scbond_it	12.934	2.833	19
X-RAY DIFFRACTION	r_scbond_other	12.609	2.774	20
X-RAY DIFFRACTION	r_scangle_it	14.861	4.13	26
X-RAY DIFFRACTION	r_scangle_other	14.583	4.05	27
X-RAY DIFFRACTION	r_lrange_it	18.747	28.484	33
X-RAY DIFFRACTION	r_lrange_other	18.717	29.582	34

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 (%)
1.705-1.749			0.374	25	X-RAY DIFFRACTION	75.7576
1.749-1.797	0.625	3	0.342	24	X-RAY DIFFRACTION	100
1.797-1.849	0.143	2	0.425	26	X-RAY DIFFRACTION	100
1.849-1.905	0.005	1	0.344	24	X-RAY DIFFRACTION	100
1.905-1.967	0.172	3	0.235	32	X-RAY DIFFRACTION	94.5946
1.967-2.036	0.376	6	0.335	27	X-RAY DIFFRACTION	80.4878
2.036-2.112	0.195	2	0.16	27	X-RAY DIFFRACTION	100
2.112-2.198	0.094	2	0.247	26	X-RAY DIFFRACTION	100
2.198-2.295	0.446	3	0.23	22	X-RAY DIFFRACTION	100
2.295-2.405	0.633	4	0.336	31	X-RAY DIFFRACTION	100
2.405-2.534	0.415	7	0.216	18	X-RAY DIFFRACTION	96.1538
2.534-2.686		0	0.358	13	X-RAY DIFFRACTION	92.8571
2.686-2.868		0	0.301	15	X-RAY DIFFRACTION	93.75
2.868-3.094	0.063	2	0.273	23	X-RAY DIFFRACTION	100
3.094-3.383	0.751	1	0.245	17	X-RAY DIFFRACTION	100
3.383-3.773	0.13	4	0.141	11	X-RAY DIFFRACTION	100
3.773-4.337	0.219	2	0.151	17	X-RAY DIFFRACTION	95
4.337-5.265	0.185	2	0.117	15	X-RAY DIFFRACTION	100
5.265-7.26		0	0.395	4	X-RAY DIFFRACTION	100
7.26-23.086	0.069	1	0.281	6	X-RAY DIFFRACTION	87.5

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