9JVR | pdb_00009jvr

De novo designed GFP 1GFL-15

PDB DOI: https://doi.org/10.2210/pdb9JVR/pdb

Classification: DE NOVO PROTEIN
Organism(s): synthetic construct
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2024-10-09 Released: 2025-10-15
Deposition Author(s): Guo, Z., Liu, J.L., Lai, L.H.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.61 Å
R-Value Free:
0.300 (Depositor), 0.299 (DCC)
R-Value Work:
0.247 (Depositor), 0.247 (DCC)
R-Value Observed:
0.249 (Depositor)

Starting Model: in silico
View more details

wwPDB Validation 3D Report Full Report

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

Literature

Atomic protein design using geometric deep learning

Liu, J.L., Guo, Z., Lai, L.H.

To be published.

Macromolecule Content

Total Structure Weight: 108.27 kDa
Atom Count: 7,402
Modeled Residue Count: 912
Deposited Residue Count: 948
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
De novo designed 1GFL-15	A, B, C, D	237	synthetic construct	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
GYS Query on GYS	A, B, C, D	L-PEPTIDE LINKING	C₁₄ H₁₅ N₃ O₅		SER, TYR, GLY

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.61 Å
R-Value Free: 0.300 (Depositor), 0.299 (DCC)
R-Value Work: 0.247 (Depositor), 0.247 (DCC)
R-Value Observed: 0.249 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.698	α = 70.305
b = 65.798	β = 89.843
c = 88.491	γ = 74.356

Software Package:

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

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2025-10-15

Deposition Author(s):

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

Revision History (Full details and data files)

Version 1.0: 2025-10-15
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 R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.