7RHB

A new fluorescent protein darkmRuby at pH 8.0

PDB DOI: https://doi.org/10.2210/pdb7RHB/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: 2.51 Å
R-Value Free: 0.266
R-Value Work: 0.227
R-Value Observed: 0.229

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

A Long-range Interaction Affects Brightness and pH Stability of a Dark Fluorescent Protein

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

To be published.

Macromolecule Content

Total Structure Weight: 53.02 kDa
Atom Count: 3,632
Modelled Residue Count: 440
Deposited Residue Count: 470
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
darkmRuby	A [auth B], B [auth A]	235	Entacmaea quadricolor	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

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: 2.51 Å
R-Value Free: 0.266
R-Value Work: 0.227
R-Value Observed: 0.229
Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 108.087	α = 90
b = 77.268	β = 92.11
c = 66.808	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

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

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.