6GRZ | pdb_00006grz

Crystal structure of the light chain dimer mH6

PDB DOI: https://doi.org/10.2210/pdb6GRZ/pdb

Classification: IMMUNE SYSTEM
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2018-06-13 Released: 2019-06-12
Deposition Author(s): Maritan, M., Ricagno, S., Ambrosetti, A., Oberti, L.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free:
0.238 (Depositor), 0.245 (DCC)
R-Value Work:
0.206 (Depositor)
R-Value Observed:
0.208 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

Inherent Biophysical Properties Modulate the Toxicity of Soluble Amyloidogenic Light Chains

Maritan, M., Romeo, M., Oberti, L., Sormanni, P., Tasaki, M., Russo, R., Ambrosetti, A., Motta, P., Rognoni, P., Mazzini, G., Barbiroli, A., Palladini, G., Vendruscolo, M., Diomede, L., Bolognesi, M., Merlini, G., Lavatelli, F., Ricagno, S.

(2020) J Mol Biology

DOI: https://doi.org/10.1016/j.jmb.2019.12.015

Macromolecule Content

Total Structure Weight: 46.13 kDa
Atom Count: 3,341
Modeled Residue Count: 429
Deposited Residue Count: 432
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
mH6	A, B	216	Homo sapiens	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth B] SDF format, chain G [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth B] MOL2 format, chain G [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth B] mmCIF format, chain G [auth B]	C [auth A], D [auth A], E [auth A], F [auth B], G [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.238 (Depositor), 0.245 (DCC)
R-Value Work: 0.206 (Depositor)
R-Value Observed: 0.208 (Depositor)

Space Group: I 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79.887	α = 90
b = 72.578	β = 105.67
c = 84.836	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

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View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2019-06-12

Deposition Author(s):

Funding Organization	Location	Grant Number
	Italy	2016-0489

Revision History (Full details and data files)

Version 1.0: 2019-06-12
Type: Initial release
Version 1.1: 2020-08-26
Changes: Database references
Version 1.2: 2024-01-17
Changes: Data collection, Database references, Refinement description
Version 1.3: 2024-11-06
Changes: Structure summary