6XYM | pdb_00006xym

Nbe-LBM

PDB DOI: https://doi.org/10.2210/pdb6XYM/pdb

Classification: IMMUNE SYSTEM
Organism(s): Lama glama
Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
Mutation(s): No

Deposited: 2020-01-30 Released: 2021-02-10
Deposition Author(s): Pompidor, G., Zimmermann, S., Loew, C., Schneider, T.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.20 Å
R-Value Free:
0.198 (Depositor), 0.206 (DCC)
R-Value Work:
0.154 (Depositor), 0.163 (DCC)
R-Value Observed:
0.156 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 6XYM

This is version 1.1 of the entry. See complete history.

Literature

Engineered nanobodies with a lanthanide binding motif for crystallographic phasing

Pompidor, G., Zimmermann, S., Loew, C., Schneider, T.

To be published.

Macromolecule Content

Total Structure Weight: 31.48 kDa
Atom Count: 2,364
Modeled Residue Count: 270
Deposited Residue Count: 286
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nbe-LBM	A, B	143	Lama glama	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
TB (Subject of Investigation/LOI) Query on TB Download:Ideal Coordinates CCD File SDF format, chain D [auth B] SDF format, chain C [auth A] MOL2 format, chain D [auth B] MOL2 format, chain C [auth A] mmCIF format, chain D [auth B] mmCIF format, chain C [auth A]	C [auth A], D [auth B]	TERBIUM(III) ION Tb HKCRVXUAKWXBLE-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.20 Å
R-Value Free: 0.198 (Depositor), 0.206 (DCC)
R-Value Work: 0.154 (Depositor), 0.163 (DCC)
R-Value Observed: 0.156 (Depositor)

Space Group: P 2 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.731	α = 90
b = 63.855	β = 90
c = 66.792	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PDB_EXTRACT	data extraction
SHELXDE	phasing

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2021-02-10

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2021-02-10
Type: Initial release
Version 1.1: 2024-11-13
Changes: Data collection, Database references, Structure summary

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.