6Y1R | pdb_00006y1r

Nb22-LBT

PDB DOI: https://doi.org/10.2210/pdb6Y1R/pdb

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

Deposited: 2020-02-13 Released: 2021-02-24
Deposition Author(s): Pompidor, G., Zimmermann, S., Loew, C., Schneider, T.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.85 Å
R-Value Free:
0.234 (Depositor), 0.236 (DCC)
R-Value Work:
0.204 (Depositor), 0.205 (DCC)
R-Value Observed:
0.206 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 6Y1R

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: 82.4 kDa
Atom Count: 5,588
Modeled Residue Count: 685
Deposited Residue Count: 735
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nb22-LBT	A, B, C, D, E	147	Lama glama	Mutation(s): 0

Small Molecules

Ligands 2 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 F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth B] SDF format, chain K [auth C] SDF format, chain N [auth C] SDF format, chain O [auth D] SDF format, chain R [auth E] SDF format, chain S [auth E] SDF format, chain J [auth C] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth B] MOL2 format, chain K [auth C] MOL2 format, chain N [auth C] MOL2 format, chain O [auth D] MOL2 format, chain R [auth E] MOL2 format, chain S [auth E] MOL2 format, chain J [auth C] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth B] mmCIF format, chain K [auth C] mmCIF format, chain N [auth C] mmCIF format, chain O [auth D] mmCIF format, chain R [auth E] mmCIF format, chain S [auth E] mmCIF format, chain J [auth C]	F [auth A] G [auth A] H [auth B] J [auth C] K [auth C] F [auth A], G [auth A], H [auth B], J [auth C], K [auth C], N [auth C], O [auth D], R [auth E], S [auth E]	TERBIUM(III) ION Tb HKCRVXUAKWXBLE-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain K [auth C] Focus chain N [auth C] Focus chain O [auth D] Focus chain R [auth E] Focus chain S [auth E] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain K [auth C] Focus chain N [auth C] Focus chain O [auth D] Focus chain R [auth E] Focus chain S [auth E]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain I [auth B] SDF format, chain L [auth C] SDF format, chain P [auth D] SDF format, chain Q [auth D] SDF format, chain T [auth E] SDF format, chain M [auth C] MOL2 format, chain I [auth B] MOL2 format, chain L [auth C] MOL2 format, chain P [auth D] MOL2 format, chain Q [auth D] MOL2 format, chain T [auth E] MOL2 format, chain M [auth C] mmCIF format, chain I [auth B] mmCIF format, chain L [auth C] mmCIF format, chain P [auth D] mmCIF format, chain Q [auth D] mmCIF format, chain T [auth E] mmCIF format, chain M [auth C]	I [auth B] L [auth C] M [auth C] P [auth D] Q [auth D] I [auth B], L [auth C], M [auth C], P [auth D], Q [auth D], T [auth E]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain I [auth B] Focus chain L [auth C] Focus chain M [auth C] Focus chain P [auth D] Focus chain Q [auth D] Focus chain T [auth E] Interactions & Density Focus chain I [auth B] Focus chain L [auth C] Focus chain M [auth C] Focus chain P [auth D] Focus chain Q [auth D] Focus chain T [auth E]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.85 Å
R-Value Free: 0.234 (Depositor), 0.236 (DCC)
R-Value Work: 0.204 (Depositor), 0.205 (DCC)
R-Value Observed: 0.206 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.469	α = 91.71
b = 49.425	β = 99.18
c = 81.349	γ = 102.61

Software Package:

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

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2021-02-24

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2021-02-24
Type: Initial release
Version 1.1: 2024-10-23
Changes: Data collection, Database references, Structure summary

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

CoreTrustSeal

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.