6QD6 | pdb_00006qd6

Molecular scaffolds expand the nanobody toolkit for cryo-EM applications: crystal structure of Mb-cHopQ-Nb207

PDB DOI: https://doi.org/10.2210/pdb6QD6/pdb

Classification: STRUCTURAL PROTEIN
Organism(s): Helicobacter pylori, Helicobacter pylori G27
Expression System: Escherichia coli
Mutation(s): No
Membrane Protein: Yes mpstruc

Deposited: 2018-12-31 Released: 2019-12-18
Deposition Author(s): Uchanski, T., Masiulis, S., Fischer, B., Kalichuk, V., Wohlkonig, A., Zogg, T., Remaut, H., Vranken, W., Aricescu, A.R., Pardon, E., Steyaert, J.
Funding Organization(s): Research Foundation - Flanders, Grenoble Instruct-ERIC Center

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.84 Å
R-Value Free:
0.239 (Depositor), 0.252 (DCC)
R-Value Work:
0.204 (Depositor), 0.226 (DCC)
R-Value Observed:
0.206 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Megabodies expand the nanobody toolkit for protein structure determination by single-particle cryo-EM

Uchanski, T., Masiulis, S., Fischer, B., Kalichuk, V., Lopez-Sanchez, U., Zarkadas, E., Weckener, M., Sente, A., Ward, P., Wohlkonig, A., Zogg, T., Remaut, H., Naismith, J.H., Nury, H., Vranken, W., Aricescu, A.R., Pardon, E., Steyaert, J.

(2021) Nat Methods 18

DOI: https://doi.org/10.1038/s41592-020-01001-6

Macromolecule Content

Total Structure Weight: 580.53 kDa
Atom Count: 33,077
Modeled Residue Count: 4,346
Deposited Residue Count: 5,420
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mb-cHopQ-Nb207,Outer membrane protein,Mb-cHopQ-Nb207,Outer membrane protein,Mb-cHopQ-Nb207	A, B, C, D, E A, B, C, D, E, F, G, H, I, J	542	Helicobacter pylori, Helicobacter pylori G27	Mutation(s): 0 Gene Names: C2R84_04360, hopQ, HPG27_1120 Membrane Entity: Yes
UniProt
Find proteins for B5Z8H1 (Helicobacter pylori (strain G27)) Explore B5Z8H1 Go to UniProtKB: B5Z8H1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	B5Z8H1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain K [auth A] MOL2 format, chain K [auth A] mmCIF format, chain K [auth A]	K [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain K [auth A] Interactions & Density Focus chain K [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.84 Å
R-Value Free: 0.239 (Depositor), 0.252 (DCC)
R-Value Work: 0.204 (Depositor), 0.226 (DCC)
R-Value Observed: 0.206 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.17	α = 92.05
b = 92.92	β = 96.93
c = 244.22	γ = 112.15

Software Package:

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

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2019-12-18

Deposition Author(s):

Funding Organization	Location	Grant Number
Research Foundation - Flanders	Belgium	--
Grenoble Instruct-ERIC Center	Belgium	--

Revision History (Full details and data files)

Version 1.0: 2019-12-18
Type: Initial release
Version 1.1: 2021-01-13
Changes: Database references
Version 1.2: 2024-11-13
Changes: Data collection, Database references, Structure summary