6XZF | pdb_00006xzf

Nanobody in complex with eGFP

PDB DOI: https://doi.org/10.2210/pdb6XZF/pdb

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

Deposited: 2020-02-04 Released: 2021-02-17
Deposition Author(s): Pompidor, G., Zimmermann, S., Loew, C., Schneider, T.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free:
0.203 (Depositor), 0.206 (DCC)
R-Value Work:
0.173 (Depositor), 0.176 (DCC)
R-Value Observed:
0.175 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 6XZF

This is version 2.1 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: 41.85 kDa
Atom Count: 3,055
Modeled Residue Count: 352
Deposited Residue Count: 368
Unique protein chains: 2

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
eGFP	A	236	Aequorea victoria	Mutation(s): 0
UniProt
Find proteins for P42212 (Aequorea victoria) Explore P42212 Go to UniProtKB: P42212
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P42212
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Nanobody targeted against eGFP	B	132	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 C [auth B] MOL2 format, chain C [auth B] mmCIF format, chain C [auth B]	C [auth B]	TERBIUM(III) ION Tb HKCRVXUAKWXBLE-UHFFFAOYSA-N		Interactions Focus chain C [auth B] Interactions & Density Focus chain C [auth B]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CRO Query on CRO	A	L-PEPTIDE LINKING	C₁₅ H₁₇ N₃ O₅		THR, TYR, GLY

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.203 (Depositor), 0.206 (DCC)
R-Value Work: 0.173 (Depositor), 0.176 (DCC)
R-Value Observed: 0.175 (Depositor)

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.335	α = 90
b = 69.335	β = 90
c = 169.063	γ = 120

Software Package:

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

Structure Validation

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Entry History

Deposition Data

Released Date: 2021-02-17

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2021-02-17
Type: Initial release
Version 2.0: 2023-11-15
Changes: Advisory, Atomic model, Data collection, Database references
Version 2.1: 2024-10-23
Changes: 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.