8SG3

High Affinity nanobodies against GFP

PDB DOI: https://doi.org/10.2210/pdb8SG3/pdb

Classification: IMMUNE SYSTEM
Organism(s): Aequorea victoria, Lama glama
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2023-04-11 Released: 2024-05-22
Deposition Author(s): Ketaren, N.E., Rout, M.P., Bonanno, J.B., Almo, S.C.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.11 Å
R-Value Free: 0.303
R-Value Work: 0.273
R-Value Observed: 0.276

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

High Affinity nanobodies against GFP

Ketaren, N.E., Rout, M.P., Almo, S.

To be published.

Macromolecule Content

Total Structure Weight: 44.29 kDa
Atom Count: 2,779
Modelled Residue Count: 352
Deposited Residue Count: 394
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Green fluorescent protein	A	253	Aequorea victoria	Mutation(s): 1 Gene Names: GFP
UniProt
Find proteins for P42212 (Aequorea victoria) Explore P42212 Go to UniProtKB: P42212
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P42212
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
LaG41	B	141	Lama glama	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CR2 Query on CR2	A	L-PEPTIDE LINKING	C₁₃ H₁₃ N₃ O₄		GLY, TYR, GLY

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.11 Å
R-Value Free: 0.303
R-Value Work: 0.273
R-Value Observed: 0.276
Space Group: I 4₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 108.633	α = 90
b = 108.633	β = 90
c = 198.744	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
SCALEPACK	data scaling
DENZO	data reduction
PHASER	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2024-05-22

Deposition Author(s):

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	--

Revision History (Full details and data files)

Version 1.0: 2024-05-22
Type: Initial release

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 R01GM133198.