8YQ4 | pdb_00008yq4

Structure of mBaoJin2

PDB DOI: https://doi.org/10.2210/pdb8YQ4/pdb

Classification: FLUORESCENT PROTEIN
Organism(s): Cytaeis uchidae
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2024-03-19 Released: 2024-03-27
Deposition Author(s): Boyko, K.M., Nikolaeva, A.Y., Minyaev, M.E., Kuzmicheva, T.P., Vlaskina, A.V., Popov, V.O., Pyatkevich, K.D., Subach, F.V.
Funding Organization(s): Russian Science Foundation

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free:
0.208 (Depositor), 0.215 (DCC)
R-Value Work:
0.170 (Depositor), 0.179 (DCC)
R-Value Observed:
0.172 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 8YQ4

This is version 2.0 of the entry. See complete history.

Literature

Structure of mBaoJin2

Boyko, K.M., Nikolaeva, A.Y., Minyaev, M.E., Kuzmicheva, T.P., Vlaskina, A.V., Popov, V.O., Pyatkevich, K.D., Subach, F.V.

To be published.

Macromolecule Content

Total Structure Weight: 53.59 kDa
Atom Count: 3,776
Modeled Residue Count: 428
Deposited Residue Count: 464
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
mBaoJin2 - bright and stable green fluorescent protein	A [auth B], B [auth A]	232	Cytaeis uchidae	Mutation(s): 0
UniProt
Find proteins for A0A8S0GSD4 (Cytaeis uchidae) Explore A0A8S0GSD4 Go to UniProtKB: A0A8S0GSD4
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A8S0GSD4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain C [auth B] MOL2 format, chain F [auth A] MOL2 format, chain C [auth B] mmCIF format, chain F [auth A] mmCIF format, chain C [auth B]	C [auth B], F [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain C [auth B] Focus chain F [auth A] Interactions & Density Focus chain C [auth B] Focus chain F [auth A]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain D [auth B] MOL2 format, chain D [auth B] mmCIF format, chain D [auth B]	D [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain D [auth B] Interactions & Density Focus chain D [auth B]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain E [auth B] MOL2 format, chain G [auth A] MOL2 format, chain E [auth B] mmCIF format, chain G [auth A] mmCIF format, chain E [auth B]	E [auth B], G [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain E [auth B] Focus chain G [auth A] Interactions & Density Focus chain E [auth B] Focus chain G [auth A]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CR2 Query on CR2	A [auth B], B [auth A]	L-PEPTIDE LINKING	C₁₃ H₁₃ N₃ O₄		GLY, TYR, GLY

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.208 (Depositor), 0.215 (DCC)
R-Value Work: 0.170 (Depositor), 0.179 (DCC)
R-Value Observed: 0.172 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.139	α = 90
b = 120.298	β = 106.36
c = 52.915	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
CrysalisPro	data reduction
MOLREP	phasing

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2024-03-27

Deposition Author(s):

Nikolaeva, A.Y.

Kuzmicheva, T.P.

Pyatkevich, K.D.

Funding Organization	Location	Grant Number
Russian Science Foundation	Russian Federation	21-74-20135

Revision History (Full details and data files)

Version 1.0: 2024-03-27
Type: Initial release
Version 1.1: 2024-11-06
Changes: Structure summary
Version 2.0: 2026-03-18
Changes: Polymer sequence

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.