6R27

Crystallographic superstructure of the photosensory core module (PAS-GAF-PHY) of the bacterial phytochrome Agp1 (AtBphP1) locked in a Pr-like state

• PDB DOI: https://doi.org/10.2210/pdb6R27/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Agrobacterium fabrum str. C58
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2019-03-15 Released: 2020-04-01 
• Deposition Author(s): Scheerer, P., Michael, N., Lamparter, T., Krauss, N.
• Funding Organization(s): German Research Foundation

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.40 Å
• R-Value Free: 0.297 
• R-Value Work: 0.255 
• R-Value Observed: 0.257 

Literature

Crystal structures of the photosensory core module of bacteriophytochrome Agp1 reveal pronounced structural flexibility of this protein in the red-absorbing Pr state

Scheerer, P., Schmidt, A., Nagano, S., Qureshi, B., Szczepek, M., Sauthof, L., Michael, N., Inomata, K., Lamparter, T., Krauss, N.

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 and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 228.25 kDa 
• Atom Count: 14,122 
• Modelled Residue Count: 1,876 
• Deposited Residue Count: 2,040 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bacteriophytochrome protein	A, B, C, D	510	Agrobacterium fabrum str. C58	Mutation(s): 0  Gene Names: Atu1990
UniProt
Find proteins for Q7CY45 (Agrobacterium fabrum (strain C58 / ATCC 33970)) Explore Q7CY45  Go to UniProtKB:  Q7CY45

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
JQ2 (Subject of Investigation/LOI)	E [auth A], F [auth B], G [auth C], H [auth D]	3-[2-[(~{Z})-[12-ethyl-6-(3-hydroxy-3-oxopropyl)-13-methyl-11-oxidanylidene-4,10-diazatricyclo[8.3.0.0^{3,7}]trideca-1,3,6,12-tetraen-5-ylidene]methyl]-5-[(~{Z})-(3-ethyl-4-methyl-5-oxidanylidene-pyrrol-2-ylidene)methyl]-4-methyl-1~{H}-pyrrol-3-yl]propanoic acid C34 H38 N4 O6 ZPENGPJFMYEJSJ-DPTABBBISA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B, C, D	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.40 Å
• R-Value Free: 0.297 
• R-Value Work: 0.255 
• R-Value Observed: 0.257 
• Space Group: I 4 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 240.218	α = 90
b = 240.218	β = 90
c = 160.515	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing
Coot	model building

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-04-01 
Deposition Author(s): Scheerer, P., Michael, N., Lamparter, T., Krauss, N.

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Funding Organization	Location	Grant Number
German Research Foundation	Germany	SFB498-B2
German Research Foundation	Germany	SFB1078-B6
German Research Foundation	Germany	LA 799/18-1
German Research Foundation	Germany	KR 2034/1-1
German Research Foundation	Germany	DFG under Germanys Excellence Strategy - UniSysCat - 390540038
German Research Foundation	Germany	DFG Cluster of Excellence - UniCat

Revision History  

• Version 1.0: 2020-04-01
  Type: Initial release
  
• Version 1.1: 2024-01-24
  Changes: Data collection, Database references, Refinement description