31JT | pdb_000031jt

SFX structure of non-photoactivated PAmCherry1

PDB DOI: https://doi.org/10.2210/pdb31JT/pdb

Classification: FLUORESCENT PROTEIN
Organism(s): Discosoma sp.
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2026-06-09 Released: 2026-09-23
Deposition Author(s): Bibi, H., De Vrieze, L., De Zitter, E., Coquelle, N., Kamata, K., Luo, F., Nango, E., Mizuno, H.
Funding Organization(s): KU Leuven, Research Foundation - Flanders (FWO)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.63 Å
R-Value Free:
0.194 (Depositor), 0.195 (DCC)
R-Value Work:
0.163 (Depositor), 0.163 (DCC)
R-Value Observed:
0.165 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

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

Literature

Direct visualization of hydroperoxy intermediate in fluorescent protein chromophore maturation in PAmCherry1

Bibi, H., De Vrieze, L., De Zitter, E., Coquelle, N., Kamata, K., Luo, F., Nango, E., Mizuno, H.

To be published.

Macromolecule Content

Total Structure Weight: 56.38 kDa
Atom Count: 4,486
Modeled Residue Count: 452
Deposited Residue Count: 486
Unique protein chains: 1

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PAmCherry1 protein	A, B	242	Discosoma sp.	Mutation(s): 1 Gene Names: PAmCherry, PAmCherry1
UniProt
Find proteins for D1MPT3 (Discosoma sp.) Explore D1MPT3 Go to UniProtKB: D1MPT3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	D1MPT3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A] mmCIF format, chain G [auth A]	G [auth A]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain I [auth B] SDF format, chain J [auth B] SDF format, chain K [auth B] SDF format, chain L [auth B] SDF format, chain M [auth B] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain I [auth B] mmCIF format, chain J [auth B] mmCIF format, chain K [auth B] mmCIF format, chain L [auth B] mmCIF format, chain M [auth B]	D [auth A] E [auth A] F [auth A] I [auth B] J [auth B] D [auth A], E [auth A], F [auth A], I [auth B], J [auth B], K [auth B], L [auth B], M [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B]
OXY Query on OXY Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain H [auth B] MOL2 format, chain C [auth A] MOL2 format, chain H [auth B] mmCIF format, chain C [auth A] mmCIF format, chain H [auth B]	C [auth A], H [auth B]	OXYGEN MOLECULE O₂ MYMOFIZGZYHOMD-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain H [auth B] Interactions & Density Focus chain C [auth A] Focus chain H [auth B]

Modified Residues 2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
A1J9N Query on A1J9N	A, B	L-PEPTIDE LINKING	C₁₆ H₁₉ N₃ O₆ S		MET, TYR, GLY
A1KPX Query on A1KPX	A, B	L-PEPTIDE LINKING	C₁₆ H₁₉ N₃ O₄ S		MET, TYR, GLY

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.63 Å
R-Value Free: 0.194 (Depositor), 0.195 (DCC)
R-Value Work: 0.163 (Depositor), 0.163 (DCC)
R-Value Observed: 0.165 (Depositor)

Space Group: P 2 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 39.36	α = 90
b = 79.16	β = 90
c = 145.4	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
CrystFEL	data reduction
CrystFEL	data scaling
PHENIX	phasing

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2026-09-23

Deposition Author(s):

Funding Organization	Location	Grant Number
KU Leuven	Belgium	C14/22/087
Research Foundation - Flanders (FWO)	Belgium	G0A8523N
Research Foundation - Flanders (FWO)	Belgium	K801024N
Research Foundation - Flanders (FWO)	Belgium	1152226N