6MYB

Room-temperature structure of deuterated Tetdron (isomorph 1)

PDB DOI: https://doi.org/10.2210/pdb6MYB/pdb

Classification: FLUORESCENT PROTEIN
Organism(s): Echinophyllia sp. SC22
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2018-11-01 Released: 2019-11-06
Deposition Author(s): Dajnowicz, S., Kovalevsky, A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.250
R-Value Work: 0.199
R-Value Observed: 0.202

wwPDB Validation 3D Report Full Report

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

Literature

Room-temperature in crystallo photo-induced deprotonation and tetramerization of photo-switchable protein Padron2.0

Dajnowicz, S., Langan, P.S., Weiss, K.L., Ivanov, I.N., Kovalevsky, A.

To be published.

Macromolecule Content

Total Structure Weight: 203.65 kDa
Atom Count: 14,664
Modelled Residue Count: 1,728
Deposited Residue Count: 1,784
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Photoswitchable protein Tetdron	A, B, C, D, E A, B, C, D, E, F, G, H	223	Echinophyllia sp. SC22	Mutation(s): 0 Gene Names: Dronpa
UniProt
Find proteins for Q5TLG6 (Echinophyllia sp. SC22) Explore Q5TLG6 Go to UniProtKB: Q5TLG6
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q5TLG6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
GYC Query on GYC	A, B, C, D, E A, B, C, D, E, F, G, H	L-PEPTIDE LINKING	C₁₄ H₁₅ N₃ O₄ S		CYS, TYR, GLY

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.250
R-Value Work: 0.199
R-Value Observed: 0.202
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.623	α = 90
b = 129.573	β = 105.36
c = 98.564	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHENIX	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2019-11-06

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2019-11-06
Type: Initial release
Version 1.1: 2020-11-18
Changes: Structure summary
Version 2.0: 2023-11-15
Changes: Atomic model, Data collection, Database references, Derived calculations

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.