8CO5

The surface-engineered photosensory module (PAS-GAF-PHY) of the bacterial phytochrome Agp1 (AtBphP1) in the Pr form with parallel dimer formation

PDB DOI: https://doi.org/10.2210/pdb8CO5/pdb

Classification: SIGNALING PROTEIN
Organism(s): Agrobacterium fabrum str. C58
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2023-02-27 Released: 2024-03-06
Deposition Author(s): Schmidt, A., Sauthof, L., Krauss, N., Scheerer, P.
Funding Organization(s): German Research Foundation (DFG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.42 Å
R-Value Free: 0.252
R-Value Work: 0.212
R-Value Observed: 0.214

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Crystal structures of a bacterial phytochrome exhibiting a group-subgroup relationship reveal pronounced flexibility of the photosensory core module in the Pr state

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

To be published.

Macromolecule Content

Total Structure Weight: 55.35 kDa
Atom Count: 3,663
Modelled Residue Count: 475
Deposited Residue Count: 503
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bacteriophytochrome protein	A	503	Agrobacterium fabrum str. C58	Mutation(s): 4 Gene Names: Atu1990 EC: 2.7.13.3
UniProt
Find proteins for Q7CY45 (Agrobacterium fabrum (strain C58 / ATCC 33970)) Explore Q7CY45 Go to UniProtKB: Q7CY45
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q7CY45
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
V8U (Subject of Investigation/LOI) Query on V8U Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	3-[5-[(4-ethenyl-3-methyl-5-oxidanylidene-pyrrol-2-yl)methyl]-2-[[5-[(3-ethyl-4-methyl-5-oxidanylidene-pyrrol-2-yl)methyl]-3-(3-hydroxy-3-oxopropyl)-4-methyl-1~{H}-pyrrol-2-yl]methyl]-4-methyl-1~{H}-pyrrol-3-yl]propanoic acid C₃₃ H₃₈ N₄ O₆ UETWWFBMDBJSDH-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.42 Å
R-Value Free: 0.252
R-Value Work: 0.212
R-Value Observed: 0.214
Space Group: I 4 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 172.477	α = 90
b = 172.477	β = 90
c = 78.82	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2024-03-06

Deposition Author(s):

Funding Organization	Location	Grant Number
German Research Foundation (DFG)	Germany	SFB1078

Revision History (Full details and data files)

Version 1.0: 2024-03-06
Type: Initial release
Version 1.1: 2024-10-09
Changes: Structure summary

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), 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 R01GM157729.