9X27 | pdb_00009x27

X-ray Structure of the EGFP:GBPR(R34K) Complex

PDB DOI: https://doi.org/10.2210/pdb9X27/pdb

Classification: FLUORESCENT PROTEIN
Organism(s): Aequorea victoria, Vicugna pacos
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2025-10-03 Released: 2026-10-07
Deposition Author(s): Chen, X., Wu, D.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free:
0.320 (Depositor), 0.320 (DCC)
R-Value Work:
0.264 (Depositor), 0.264 (DCC)
R-Value Observed:
0.266 (Depositor)

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

Validation slider image for 9X27

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

Literature

Precise Chemogenetic Programming of Nanobodies for Imaging, Therapeutics, and Optogenetics

Chen, X., Wu, D., Zhou, C., Xia, S., Xi, R., Dai, Q., He, Y.

To be published.

Macromolecule Content

Total Structure Weight: 77.06 kDa
Atom Count: 5,492
Modeled Residue Count: 685
Deposited Residue Count: 686
Unique protein chains: 2

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Green fluorescent protein	A, B	226	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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P42212
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
GBPR(R34K)	C, D	117	Vicugna pacos	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.320 (Depositor), 0.320 (DCC)
R-Value Work: 0.264 (Depositor), 0.264 (DCC)
R-Value Observed: 0.266 (Depositor)

Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 151.246	α = 90
b = 151.246	β = 90
c = 73.137	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2026-10-07

Deposition Author(s):

Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	32071410

Revision History (Full details and data files)

Version 1.0: 2026-10-07
Type: Initial release