4Y3I

PAS-GAF fragment from Deinococcus radiodurans BphP assembled with BV - Y307S, low dose

• PDB DOI: https://doi.org/10.2210/pdb4Y3I/pdb

• Classification: TRANSFERASE
• Organism(s): Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2015-02-10 Released: 2015-05-20 
• Deposition Author(s): Li, F., Burgie, E.S., Yu, T., Heroux, A., Schatz, G.C., Vierstra, R.D., Orville, A.M.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), Department of Energy (DOE, United States), National Science Foundation (NSF, United States)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.69 Å
• R-Value Free: 0.226 
• R-Value Work: 0.190 
• R-Value Observed: 0.192 

Starting Model: experimental

Literature

X-ray radiation induces deprotonation of the bilin chromophore in crystalline D. radiodurans phytochrome.

Li, F., Burgie, E.S., Yu, T., Heroux, A., Schatz, G.C., Vierstra, R.D., Orville, A.M.

(2015) J Am Chem Soc 137: 2792-2795

• PubMed: 25650486 
• DOI: https://doi.org/10.1021/ja510923m
• Primary Citation of Related Structures:  
  4Y3I, 4Y5F


• PubMed Abstract: 
  

  We report that in the red light-absorbing (Pr) state, the bilin chromophore of the Deinococcus radiodurans proteobacterial phytochrome (DrBphP) is hypersensitive to X-ray photons used in typical synchrotron X-ray protein crystallography experiments. This causes the otherwise fully protonated chromophore to deprotonate without additional major structural changes. These results have major implications for our understanding of the structural and chemical characteristics of the resting and intermediate states of phytochromes and other photoreceptor proteins.

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Organizational Affiliation: 

Photon Sciences Directorate and ∥Biosciences Department, Brookhaven National Laboratory , Upton, New York 11973, United States.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 35.05 kDa 
• Atom Count: 2,693 
• Modelled Residue Count: 319 
• Deposited Residue Count: 319 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bacteriophytochrome	A	319	Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539	Mutation(s): 1  Gene Names: bphP, DR_A0050 EC: 2.7.13.3
UniProt
Find proteins for Q9RZA4 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 / NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1)) Explore Q9RZA4  Go to UniProtKB:  Q9RZA4

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
LBV	B [auth A]	3-[2-[(Z)-[3-(2-carboxyethyl)-5-[(Z)-(4-ethenyl-3-methyl-5-oxidanylidene-pyrrol-2-ylidene)methyl]-4-methyl-pyrrol-1-ium -2-ylidene]methyl]-5-[(Z)-[(3E)-3-ethylidene-4-methyl-5-oxidanylidene-pyrrolidin-2-ylidene]methyl]-4-methyl-1H-pyrrol-3- yl]propanoic acid C33 H37 N4 O6 DKMLMZVDTGOEGU-ISEYCTJISA-O

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.69 Å
• R-Value Free: 0.226 
• R-Value Work: 0.190 
• R-Value Observed: 0.192 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 89.481	α = 90
b = 51.917	β = 116.22
c = 80.339	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2015-05-20 
Deposition Author(s): Li, F., Burgie, E.S., Yu, T., Heroux, A., Schatz, G.C., Vierstra, R.D., Orville, A.M.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	8P41GM103473-16
Department of Energy (DOE, United States)	United States	FWP BO-70
National Science Foundation (NSF, United States)	United States	MCB-1329956
National Science Foundation (NSF, United States)	United States	CHE-1147335
Department of Energy (DOE, United States)	United States	DE-AC02-98CH10886

Revision History  

• Version 1.0: 2015-05-20
  Type: Initial release
  
• Version 1.1: 2017-09-06
  Changes: Author supporting evidence, Derived calculations, Source and taxonomy
• Version 1.2: 2019-11-27
  Changes: Author supporting evidence
• Version 1.3: 2024-10-23
  Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary