8RJO | pdb_00008rjo

Serial femtosecond X-ray structure of a fluorescence optimized bathy phytochrome PAiRFP2 derived from wild-type Agp2 in I1 intermediate state.

PDB DOI: https://doi.org/10.2210/pdb8RJO/pdb

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

Deposited: 2023-12-21 Released: 2025-05-14
Deposition Author(s): Sauthof, L., Schmidt, A., Szczepek, M., Brewster, A.S., Kern, J.F., Scheerer, P.
Funding Organization(s): German Research Foundation (DFG), Boehringer Ingelheim Fonds (BIF), Israel Science Foundation, Department of Energy (DOE, United States), National Institutes of Health/Office of the Director, Wellcome Trust, Royal Society

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.54 ?
R-Value Free:
0.236 (Depositor), 0.239 (DCC)
R-Value Work:
0.206 (Depositor), 0.210 (DCC)
R-Value Observed:
0.207 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Serial-femtosecond crystallography reveals how a phytochrome variant couples chromophore and protein structural changes

Sauthof, L., Szczepek, M., Schmidt, A., Bhowmick, A., Dasgupta, M., Mackintosh, M.J., Gul, S., Fuller, F.D., Chatterjee, R., Young, I.D., Michael, N., Heyder, N.A., Bauer, B., Koch, A., Bogacz, I., Kim, I.-S., Simon, P.S., Butryn, A., Aller, P., Chukhutsina, V.U., Baxter, J.M., Hutchison, C.D.M., Liebschner, D., Poon, B., Sauter, N.K., Miller, M.D., Phillips Jr., G.N., Alonso-Mori, R., Hunter, M.S., Batyuk, A., Owada, S., Tono, K., Tanaka, R., van Thor, J.J., Krauss, N., Lamparter, T., Brewster, A.S., Schapiro, I., Orville, A.M., Yachandra, V.K., Yano, J., Hildebrandt, P., Kern, J.F., Scheerer, P.

(2025) Sci Adv

Macromolecule Content

Total Structure Weight: 114.91 kDa
Atom Count: 7,956
Modelled Residue Count: 980
Deposited Residue Count: 1,018
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
histidine kinase	A, B	509	Agrobacterium fabrum str. C58	Mutation(s): 24 Gene Names: Atu2165 EC: 2.7.13.3
UniProt
Find proteins for A9CI81 (Agrobacterium fabrum (strain C58 / ATCC 33970)) Explore A9CI81 Go to UniProtKB: A9CI81
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A9CI81
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EL5 (Subject of Investigation/LOI) Query on EL5 Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain F [auth B] MOL2 format, chain C [auth A] MOL2 format, chain F [auth B] mmCIF format, chain C [auth A] mmCIF format, chain F [auth B]	C [auth A], F [auth B]	3-[(2Z)-2-({3-(2-carboxyethyl)-5-[(E)-(4-ethenyl-3-methyl-5-oxo-1,5-dihydro-2H-pyrrol-2-ylidene)methyl]-4-methyl-1H-pyrrol-2-yl}methylidene)-5-{(Z)-[(3E,4S)-3-ethylidene-4-methyl-5-oxopyrrolidin-2-ylidene]methyl}-4-methyl-2H-pyrrol-3-yl]propanoic acid C₃₃ H₃₆ N₄ O₆ SNHIGJASYQUMKZ-IDFYGOSVSA-N		Interactions Focus chain C [auth A] Focus chain F [auth B] Interactions & Density Focus chain C [auth A] Focus chain F [auth B]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain G [auth B] SDF format, chain H [auth B] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain G [auth B] MOL2 format, chain H [auth B] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain G [auth B] mmCIF format, chain H [auth B]	D [auth A], E [auth A], G [auth B], H [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain G [auth B] Focus chain H [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain G [auth B] Focus chain H [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.54 ?
R-Value Free: 0.236 (Depositor), 0.239 (DCC)
R-Value Work: 0.206 (Depositor), 0.210 (DCC)
R-Value Observed: 0.207 (Depositor)

Space Group: P 6₃ 2 2

Unit Cell:

Length ( ? )	Angle ( ? )
a = 185.086	α = 90
b = 185.086	β = 90
c = 182.279	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
DIALS	data scaling
DIALS	data reduction
PRIME	data scaling
PHASER	phasing
PHENIX	refinement
Coot	model building

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2025-05-14

Deposition Author(s):

Funding Organization	Location	Grant Number
German Research Foundation (DFG)	Germany	CRC1078
German Research Foundation (DFG)	Germany	CRC1423
German Research Foundation (DFG)	Germany	EXC 311 2008/1
Boehringer Ingelheim Fonds (BIF)	Germany	BIF Travel Grant
Israel Science Foundation	Israel	3131/20
Department of Energy (DOE, United States)	United States	DE-AC02-76SF00515, DE-AC02-05CH11231
National Institutes of Health/Office of the Director	United States	GM05530, GM110501, GM126289, GM117126, S10 OD023453
Wellcome Trust	United Kingdom	210734/Z/18/Z
Royal Society	United Kingdom	RSWF- R2 - 182017