4ZIN | pdb_00004zin

Genetically encoded Phenyl Azide Photochemistry Drive Positive and Negative Functional Modulation of a Red Fluorescent Protein

• PDB DOI: https://doi.org/10.2210/pdb4ZIN/pdb

• Classification: FLUORESCENT PROTEIN
• Organism(s): Anaplasma marginale
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2015-04-28 Released: 2015-09-16 
• Deposition Author(s): Reddington, S.C., Driezis, S., Hartley, A.M., Watson, P.D., Rizkallah, P.J., Jones, D.D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.67 Å
• R-Value Free: 
  0.248 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.206 (Depositor), 0.212 (DCC) 
• R-Value Observed: 
  0.208 (Depositor) 

Starting Model: experimental

Literature

Genetically encoded phenyl azide photochemistry drives positive and negative functional modulation of a red fluorescent protein

Reddington, S.C., Driezis, S., Hartley, A.M., Watson, P.D., Rizkallah, P.J., Jones, D.D.

(2015) RSC Adv 5: 77734-77738

• DOI: https://doi.org/10.1039/c5ra13552d

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 3 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 74.98 kDa 
• Atom Count: 5,669 
• Modeled Residue Count: 651 
• Deposited Residue Count: 651 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
MCherry fluorescent protein	A, B, C	217	Anaplasma marginale	Mutation(s): 1  Gene Names: mCherry

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	D [auth A], E [auth A], F [auth B], G [auth B], H [auth C], I [auth C]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
EDO	J [auth C]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Modified Residues  2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
4II	A, B, C	L-PEPTIDE LINKING	C9 H10 N4 O2		PHE
CH6	A, B, C	L-PEPTIDE LINKING	C16 H19 N3 O4 S		MET, TYR, GLY

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.67 Å
• R-Value Free:  0.248 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.206 (Depositor), 0.212 (DCC) 
• R-Value Observed: 0.208 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.28	α = 90
b = 103.43	β = 90
c = 150.72	γ = 90

Software Package:

Software Name	Purpose
Aimless	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
xia2	data reduction
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-09-16 
Deposition Author(s): Reddington, S.C., Driezis, S., Hartley, A.M., Watson, P.D., Rizkallah, P.J., Jones, D.D.

Revision History  

• Version 1.0: 2015-09-16
  Type: Initial release
  
• Version 1.1: 2018-02-07
  Changes: Database references
• Version 1.2: 2019-10-23
  Changes: Data collection, Database references
• Version 1.3: 2024-01-10
  Changes: Data collection, Database references, Refinement description
• Version 2.0: 2024-05-29
  Changes: Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Polymer sequence, Structure summary
• Version 3.0: 2026-03-18
  Changes: Polymer sequence, Structure summary