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), 0.255 (DCC)
R-Value Work:
0.204 (Depositor), 0.209 (DCC)
R-Value Observed:
0.206 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

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(by identity cutoff) | 3D Structure

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% Identity50% Identity70% Identity90% Identity95% Identity100% 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 B [auth E] SDF format, chain C [auth E] MOL2 format, chain B [auth E] MOL2 format, chain C [auth E] mmCIF format, chain B [auth E] mmCIF format, chain C [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), 0.255 (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

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Ligand Structure Quality Assessment

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 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.