PDB-5mvg: Crystal structure of non-amyloidogenic light chain dimer M7

ID or keywords:

Entry

Database: PDB / ID: 5mvg

Title

Crystal structure of non-amyloidogenic light chain dimer M7

Components

light chain dimer

Keywords

IMMUNE SYSTEM / light chain dimer / light chain amyloidosis / immunoglobulin fold / protein aggregation

Function / homology

Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta

Function and homology information

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.2 Å

Authors

Oberti, L. / Rognoni, P. / Bacarizo, J. / Bolognesi, M. / Ricagno, S.

Citation

Journal: Sci Rep / Year: 2017
Title: Concurrent structural and biophysical traits link with immunoglobulin light chains amyloid propensity.
Authors: Oberti, L. / Rognoni, P. / Barbiroli, A. / Lavatelli, F. / Russo, R. / Maritan, M. / Palladini, G. / Bolognesi, M. / Merlini, G. / Ricagno, S.

History

Deposition	Jan 16, 2017	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Dec 13, 2017	Provider: repository / Type: Initial release
Revision 1.1	Jan 17, 2024	Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2	Nov 13, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	5mvg.cif.gz	166.9 KB	Display	PDBx/mmCIF format
PDB format	pdb5mvg.ent.gz	133.2 KB	Display	PDB format
PDBx/mmJSON format	5mvg.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/mv/5mvg ftp://data.pdbj.org/pub/pdb/validation_reports/mv/5mvg	HTTPS FTP

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Related structure data

Related structure data	5m6aC 5m6iSC 5m76C 5mtlC 5mudC 5muhC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	5awn-d 5y9k-d 4m5y-1 6meg-d 5n4j-d 5bk3-3 4hk0-2 4qf1-2 5y2k-2 4odu-2 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	#21 - Sep 2001 Antibodies similarity (1) #256 - Apr 2021 SARS-CoV-2 Spike and Antibodies similarity (1)

Deposited unit

A: light chain dimer

B: light chain dimer

hetero molecules

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

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	70.721, 70.721, 171.953
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	152
Space group name H-M	P3₁21

#1: Antibody	light chain dimer Mass: 22807.176 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Plasmid details: Urine
#2: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃H₈O₃
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 258 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	Y

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.72 Å³/Da / Density % sol: 54.8 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4 Details: 0.1 M MMT (Malic acid, MES and Tris-base buffer) pH 4.0, 25% w/v PEG 1.5K

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Data collection

Diffraction	Mean temperature: 273 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.873 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 5, 2016
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.873 Å / Relative weight: 1
Reflection	Resolution: 2.2→57.7 Å / Num. obs: 26134 / % possible obs: 100 % / Redundancy: 10.9 % / B_iso Wilson estimate: 35.6 Å² / R_merge(I) obs: 0.077 / Net I/σ(I): 26
Reflection shell	Resolution: 2.2→2.27 Å / Redundancy: 11.1 % / R_merge(I) obs: 0.536 / Mean I/σ(I) obs: 4.6 / Num. unique obs: 2224 / % possible all: 100

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Processing

Software

Name	Version	Classification
BUSTER	2.10.3	refinement
iMOSFLM		data reduction
SCALA		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 5M6I

5m6i

Resolution: 2.2→25.97 Å / Cor.coef. F_o:F_c: 0.921 / Cor.coef. F_o:F_c free: 0.893 / SU R Cruickshank DPI: 0.222 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.241 / SU R_free Blow DPI: 0.189 / SU R_free Cruickshank DPI: 0.183

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.239	1377	5.28 %	RANDOM
R_work	0.207	-	-	-
obs	0.209	26059	100 %	-

Displacement parameters

B_iso mean: 47.72 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-2.0748 Å²	0 Å²	0 Å²
2-	-	-2.0748 Å²	0 Å²
3-	-	-	4.1497 Å²

Refine analyze

Luzzati coordinate error obs: 0.29 Å

Refinement step

Cycle: 1 / Resolution: 2.2→25.97 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2870	0	6	258	3134

Refine LS restraints

Refine-ID	Type	Dev ideal	Number	Restraint function	Weight
X-RAY DIFFRACTION	t_bond_d	0.007	2984	HARMONIC	2
X-RAY DIFFRACTION	t_angle_deg	1.05	4070	HARMONIC	2
X-RAY DIFFRACTION	t_dihedral_angle_d		972	SINUSOIDAL	2
X-RAY DIFFRACTION	t_incorr_chiral_ct
X-RAY DIFFRACTION	t_pseud_angle
X-RAY DIFFRACTION	t_trig_c_planes		67	HARMONIC	2
X-RAY DIFFRACTION	t_gen_planes		428	HARMONIC	5
X-RAY DIFFRACTION	t_it		2984	HARMONIC	20
X-RAY DIFFRACTION	t_nbd
X-RAY DIFFRACTION	t_omega_torsion	2.82
X-RAY DIFFRACTION	t_other_torsion	16.6
X-RAY DIFFRACTION	t_improper_torsion
X-RAY DIFFRACTION	t_chiral_improper_torsion		408	SEMIHARMONIC	5
X-RAY DIFFRACTION	t_sum_occupancies
X-RAY DIFFRACTION	t_utility_distance
X-RAY DIFFRACTION	t_utility_angle
X-RAY DIFFRACTION	t_utility_torsion
X-RAY DIFFRACTION	t_ideal_dist_contact		3369	SEMIHARMONIC	4

LS refinement shell

Resolution: 2.2→2.29 Å / Total num. of bins used: 13

	R_factor	Num. reflection	% reflection
R_free	0.2262	143	4.95 %
R_work	0.1955	2745	-
all	0.197	2888	-
obs	-	-	99.93 %

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°²)	L12 (°²)	L13 (°²)	L22 (°²)	L23 (°²)	L33 (°²)	S11 (Å °)	S12 (Å °)	S13 (Å °)	S21 (Å °)	S22 (Å °)	S23 (Å °)	S31 (Å °)	S32 (Å °)	S33 (Å °)	T11 (Å²)	T12 (Å²)	T13 (Å²)	T22 (Å²)	T23 (Å²)	T33 (Å²)	Origin x (Å)	Origin y (Å)	Origin z (Å)
1	-0.3612	0.1818	-1.5737	0.7757	-5.2841	6.2469	-0.0326	-0.1241	0.0736	0.2359	-0.0242	-0.1856	-0.0359	0.0471	0.0569	-0.1526	0.1154	0.0356	0.2535	-0.0073	-0.0431	23.9301	-54.597	-10.657
2	0.5967	-0.3192	-0.2616	-0.4068	-4.1214	0	-0.0042	-0.0284	-0.03	0.1025	-0.0087	0.0016	0.1736	-0.0301	0.0129	-0.0596	0.0497	0.07	0.1994	0.0755	-0.0251	26.0866	-64.526	-10.386
3	4.094	4.2135	-1.7822	8.5316	-4.6247	1.48	0.0912	-0.1878	0.0634	-0.0717	-0.004	0.1147	0.0657	0.0307	-0.0872	0.0034	0.0876	0.0935	0.0916	0.0746	0.0884	20.7333	-56.8377	-15.7945
4	3.7593	-1.0124	-1.076	2.2948	0.2053	0.9381	-0.1002	0.0427	-0.1479	-0.0805	-0.0044	0.0263	0.0817	-0.1652	0.1046	-0.2017	0.0108	-0.0227	0.141	0.0592	-0.1078	11.665	-33.7983	-24.2838
5	2.8504	0.6358	0.2436	1.4856	0.2371	1.9718	-0.0357	-0.2915	0.3053	0.099	0.0093	0.0116	-0.2012	0.0658	0.0264	-0.1428	0.0035	-0.052	0.195	0.0424	-0.0079	11.5994	-25.0716	-21.0366
6	3.3815	-0.9934	2.1034	5.3696	-5.0005	8.7059	-0.0164	0.0891	-0.469	-0.1049	0.5302	0.2717	0.5857	-0.5942	-0.5137	-0.1218	0.0293	0.0186	0.0017	0.1009	-0.0955	0.7455	-58.5988	-2.5767
7	1.79	0.2277	1.0262	3.6482	-3.355	3.3393	-0.1053	0.1699	0.0081	0.0364	0.2648	0.1561	0.2826	-0.3101	-0.1594	-0.1513	0.03	0.0215	0.0148	0.1243	-0.1718	0.5871	-54.3745	-6.8072
8	0.9207	1.0347	0.2306	4.2475	1.8056	0	0.0336	-0.0758	-0.158	-0.0021	0.0173	-0.0866	0.0687	0.1384	-0.0509	0.3159	0.0857	0.0665	0.0933	0.0304	0.0037	12.3441	-66.8667	-3.2713
9	1.5799	-0.4266	1.1395	1.3981	-1.3062	2.7266	-0.1131	0.1232	0.1875	-0.0556	0.2494	0.2803	-0.0803	-0.1189	-0.1363	-0.225	0.0046	-0.0011	0.1874	0.0564	-0.1242	1.8485	-32.9675	-28.3717
10	4.7936	0.0872	0.013	1.9998	-2.1173	3.7706	-0.0378	0.4061	-0.4856	-0.1165	0.2227	0.0766	0.1005	0.0516	-0.1849	-0.209	-0.0279	0.0022	0.1652	0.0701	-0.0627	0.3054	-37.6961	-31.6038
11	3.2728	-0.104	0.4407	1.9546	0.1793	2.071	-0.1592	0.5768	0.1549	-0.1445	-0.0494	0.0143	-0.2224	0.3229	0.2087	-0.1995	-0.0771	-0.0725	0.3723	0.176	-0.0871	-1.4673	-28.785	-39.5481

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	{ A\|10 - A\|42 }
2	X-RAY DIFFRACTION	2	{ A\|43 - A\|74 }
3	X-RAY DIFFRACTION	3	{ A\|75 - A\|102 }
4	X-RAY DIFFRACTION	4	{ A\|103 - A\|173 }
5	X-RAY DIFFRACTION	5	{ A\|174 - A\|211 }
6	X-RAY DIFFRACTION	6	{ B\|3 - B\|74 }
7	X-RAY DIFFRACTION	7	{ B\|75 - B\|90 }
8	X-RAY DIFFRACTION	8	{ B\|91 - B\|103 }
9	X-RAY DIFFRACTION	9	{ B\|104 - B\|139 }
10	X-RAY DIFFRACTION	10	{ B\|140 - B\|183 }
11	X-RAY DIFFRACTION	11	{ B\|184 - B\|211 }

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