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.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.203 (Depositor), 0.200 (DCC) 
• R-Value Work: 
  0.173 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.175 (Depositor) 

Literature

Engineered nanobodies with a lanthanide binding motif for crystallographic phasing

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

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: surface plasmon resonance

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

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

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 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
TB (Subject of Investigation/LOI)	C [auth B]	TERBIUM(III) ION Tb HKCRVXUAKWXBLE-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
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), 0.200 (DCC) 
• R-Value Work:  0.173 (Depositor), 0.170 (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

Entry History 

Deposition Data

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

Revision History  

• 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