7RHA | pdb_00007rha

A new fluorescent protein darkmRuby at pH 5.0

PDB DOI: https://doi.org/10.2210/pdb7RHA/pdb

Classification: FLUORESCENT PROTEIN
Organism(s): Entacmaea quadricolor
Expression System: Escherichia phage EcSzw-2
Mutation(s): No

Deposited: 2021-07-16 Released: 2022-07-27
Deposition Author(s): Huang, M., Ng, H.L., Zhang, S., Deng, M., Chu, J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free:
0.211 (Depositor), 0.220 (DCC)
R-Value Work:
0.176 (Depositor), 0.186 (DCC)
R-Value Observed:
0.177 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 7RHA

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

Literature

Crystal structure of a new fluorescent protein darkmRuby at pH 5.0

Huang, M., Zhang, S., Deng, M., Zou, Y., Lin, M.Z., Ng, H.L., Chu, J.

To be published.

Macromolecule Content

Total Structure Weight: 54.07 kDa
Atom Count: 4,038
Modeled Residue Count: 441
Deposited Residue Count: 470
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
darkmRuby	A [auth B], B [auth A]	235	Entacmaea quadricolor	Mutation(s): 0

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 I [auth B] SDF format, chain R [auth A] MOL2 format, chain I [auth B] MOL2 format, chain R [auth A] mmCIF format, chain I [auth B] mmCIF format, chain R [auth A]	I [auth B], R [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain I [auth B] Focus chain R [auth A] Interactions & Density Focus chain I [auth B] Focus chain R [auth A]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain C [auth B] SDF format, chain D [auth B] SDF format, chain E [auth B] SDF format, chain F [auth B] SDF format, chain G [auth B] SDF format, chain H [auth B] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain O [auth A] MOL2 format, chain C [auth B] MOL2 format, chain D [auth B] MOL2 format, chain E [auth B] MOL2 format, chain F [auth B] MOL2 format, chain G [auth B] MOL2 format, chain H [auth B] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A] mmCIF format, chain C [auth B] mmCIF format, chain D [auth B] mmCIF format, chain E [auth B] mmCIF format, chain F [auth B] mmCIF format, chain G [auth B] mmCIF format, chain H [auth B] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A] mmCIF format, chain N [auth A] mmCIF format, chain O [auth A]	C [auth B] D [auth B] E [auth B] F [auth B] G [auth B] C [auth B], D [auth B], E [auth B], F [auth B], G [auth B], H [auth B], J [auth A], K [auth A], L [auth A], M [auth A], N [auth A], O [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain C [auth B] Focus chain D [auth B] Focus chain E [auth B] Focus chain F [auth B] Focus chain G [auth B] Focus chain H [auth B] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Interactions & Density Focus chain C [auth B] Focus chain D [auth B] Focus chain E [auth B] Focus chain F [auth B] Focus chain G [auth B] Focus chain H [auth B] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A]
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain P [auth A] SDF format, chain Q [auth A] MOL2 format, chain P [auth A] MOL2 format, chain Q [auth A] mmCIF format, chain P [auth A] mmCIF format, chain Q [auth A]	P [auth A], Q [auth A]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain P [auth A] Focus chain Q [auth A] Interactions & Density Focus chain P [auth A] Focus chain Q [auth A]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
NRQ Query on NRQ	A [auth B], B [auth A]	L-PEPTIDE LINKING	C₁₆ H₁₇ N₃ O₄ S		MET, TYR, GLY

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.211 (Depositor), 0.220 (DCC)
R-Value Work: 0.176 (Depositor), 0.186 (DCC)
R-Value Observed: 0.177 (Depositor)

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.571	α = 90
b = 101.685	β = 90
c = 134.983	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2022-07-27

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2022-07-27
Type: Initial release
Version 1.1: 2023-10-18
Changes: Data collection, Refinement description
Version 1.2: 2023-11-15
Changes: Data collection
Version 2.0: 2026-03-18
Changes: Polymer sequence, Structure summary

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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.