8S1V | pdb_00008s1v

Crystal structure of full-lenght Renilla reniformis green fluorescent protein (GFP)

PDB DOI: https://doi.org/10.2210/pdb8S1V/pdb

Classification: FLUORESCENT PROTEIN
Organism(s): Renilla reniformis
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2024-02-16 Released: 2025-09-03
Deposition Author(s): Marek, M., Nemergut, M., Smrckova, A.
Funding Organization(s): Czech Science Foundation

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.94 Å
R-Value Free:
0.249 (Depositor), 0.254 (DCC)
R-Value Work:
0.204 (Depositor), 0.209 (DCC)
R-Value Observed:
0.206 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 8S1V

Ligand Structure Quality Assessment

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

Literature

Crystal structure of full-lenght Renilla reniformis green fluorescent protein (GFP)

Marek, M., Nemergut, M., Smrckova, A.

To be published.

Macromolecule Content

Total Structure Weight: 26.2 kDa
Atom Count: 1,973
Modeled Residue Count: 230
Deposited Residue Count: 231
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Green fluorescent protein	A [auth E]	231	Renilla reniformis	Mutation(s): 1 Gene Names: GFP
UniProt
Find proteins for Q963I9 (Renilla reniformis) Explore Q963I9 Go to UniProtKB: Q963I9
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q963I9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL (Subject of Investigation/LOI) Query on GOL Download:Ideal Coordinates CCD File SDF format, chain C [auth E] SDF format, chain B [auth E] MOL2 format, chain C [auth E] MOL2 format, chain B [auth E] mmCIF format, chain C [auth E] mmCIF format, chain B [auth E]	B [auth E], C [auth E]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain B [auth E] Focus chain C [auth E] Interactions & Density Focus chain B [auth E] Focus chain C [auth E]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.94 Å
R-Value Free: 0.249 (Depositor), 0.254 (DCC)
R-Value Work: 0.204 (Depositor), 0.209 (DCC)
R-Value Observed: 0.206 (Depositor)

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 82.426	α = 90
b = 82.426	β = 90
c = 82.222	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2025-09-03

Deposition Author(s):

Funding Organization	Location	Grant Number
Czech Science Foundation	Czech Republic	GA22-09853S

Revision History (Full details and data files)

Version 1.0: 2025-09-03
Type: Initial release

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

CoreTrustSeal

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.