8C3I

Dark state of PAS-GAF fragment from Deinococcus radiodurans phytochrome

• PDB DOI: https://doi.org/10.2210/pdb8C3I/pdb

• Classification: TRANSFERASE
• Organism(s): Deinococcus radiodurans
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2022-12-24 Released: 2024-01-10 
• Deposition Author(s): Madan Kumar, S., Sebastian, W.
• Funding Organization(s): European Research Council (ERC), Japan Agency for Medical Research and Development (AMED), Academy of Finland

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.196 
• R-Value Work: 0.161 
• R-Value Observed: 0.163 

Literature

Dark state of PAS-GAF fragment from Deinococcus radiodurans phytochrome

Madan Kumar, S., Sebastian, W.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 75.63 kDa 
• Atom Count: 5,183 
• Modelled Residue Count: 628 
• Deposited Residue Count: 686 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bacteriophytochrome	A [auth B], B [auth A]	343	Deinococcus radiodurans	Mutation(s): 0  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 (Subject of Investigation/LOI)	C [auth B], D [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: 2.10 Å
• R-Value Free: 0.196 
• R-Value Work: 0.161 
• R-Value Observed: 0.163 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.95	α = 90
b = 116.5	β = 90
c = 117.7	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
CrystFEL	data reduction
CrystFEL	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-01-10 
Deposition Author(s): Madan Kumar, S., Sebastian, W.

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Funding Organization	Location	Grant Number
European Research Council (ERC)	European Union	279944
Japan Agency for Medical Research and Development (AMED)	Japan	--
Academy of Finland	Finland	285461

Revision History  

• Version 1.0: 2024-01-10
  Type: Initial release