8rjp

Serial femtosecond X-ray structure of a fluorescence optimized bathy phytochrome PAiRFP2 derived from wild-type Agp2 in I2 intermediate state.

Method: X-RAY DIFFRACTION

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1. Protein Identity and Related Structures Protein Identity & Related Structures

histidine kinase

Agrobacterium fabrum str. C58

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	;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 ; × 2 SULFATE ION × 6 TRIETHYLENE GLYCOL × 2 DI(HYDROXYETHYL)ETHER × 2 CHLORIDE ION × 2 water × 2	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 2	;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 ; × 2 SULFATE ION × 6 DI(HYDROXYETHYL)ETHER × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A9CI81_AGRFC
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–502； UniProt 1–502 Author chain B； PDBConstruct 1–502； UniProt 1–502

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	8rjp
Deposition date deposition_date	2023-12-21
Structure title title	Serial femtosecond X-ray structure of a fluorescence optimized bathy phytochrome PAiRFP2 derived from wild-type Agp2 in I2 intermediate state.
Keywords keywords	fluorescent protein, phytochrome, bacteriophytochrome, intermediate, optogenetic, SIGNALING PROTEIN; SIGNALING PROTEIN
Experimental Method method	X-RAY DIFFRACTION

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

8rjp__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

8rjp__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

8rjp__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	35.41 Å
Rg (electron density)	34.46 Å
Total Rg	35.09 Å
Atom count	7642
Residues	980
Excluded volume	135440 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`8rjp__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`8rjp__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (7)

Entity 1 Entity 1 polymer

Description description	histidine kinase
Molecular weight formula_weight	57507.5 kDa
EC 编号 ec_number	2.7.13.3
Mutation mutation	;K69R, R83K, G120D, A123T, M163L, Q168E, R220P, S243N, V244F, G269D, A276V, Y270C, E294A, H303F, H333R, I336L, D349R, M351I, A386V, G409D, L419I, T469S, A487T, E494G ;
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	8001

MASTDYHVDLTNCDREPIHIPGYIQPHGCLIACDNAMRMVLRHSENCGELLGLEGDLNGRTAEDVLGKRLVHDLRNALTVTGKTTRPAMLPAMETSDGRSFDISLHRYKSTTIIEFEPSDSDTQPLGTARKMVDRIREADSVESLISRTTRLVKATLGYDRVLIYRFEEDGAGKVVSEAKQPELESFLGQYFPASDIPQQARALYLKNTLRIISDASGTPIPVLPAVDVSGEPLDLSYAHLRNFSPIHCEYLRNMGVAASMSISVIVDDALWGLIVCHHCSPRVLSMPVRIAAAMFGEFFSMFLQVLKQKRRLDTINHAHAALDRFLRLAAHRANLEELLVDSFQDFARLIPCDGVGLWVGNNWHGHGATPPHDAIPRLARFVASVSEGRVWATHALSQAIPEAEIYADTAAGMLAIPISQVKSDYLLFFRKEIVQNLNWAGNPEKSYETGPMGDRLTPRKSFAIWKESVRLQAQPWSEADREIAETARIALVGVAFHHSELMAGLEYKHHHHHH

Source Source

Source organism organism	Agrobacterium fabrum str. C58
NCBI taxonomy ID ncbi_taxonomy_id	176299
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	;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 ;
Molecular weight formula_weight	584.7 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 4 Entity 4 non-polymer

Description description	TRIETHYLENE GLYCOL
Molecular weight formula_weight	150.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 non-polymer

Description description	DI(HYDROXYETHYL)ETHER
Molecular weight formula_weight	106.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 6 Entity 6 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 7 Entity 7 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	223

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Unit-cell length a length_a	184.735 Å
Unit-cell length b length_b	184.735 Å
Unit-cell length c length_c	181.699 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	24

Space group space_group	P 63 2 2
Space-group number int_tables_number	182
Crystal system crystal_system	—

Resolution resolution	2.430 Å
Low-resolution limit resolution_low	25.640 Å
R factor r_factor	0.2032
R_work r_work	0.2023
R_free r_free	0.2337

Serial femtosecond X-ray structure of a fluorescence optimized bathy phytochrome PAiRFP2 derived from wild-type Agp2 in I2 intermediate state.

1. Protein Identity and Related Structures Protein Identity & Related Structures

histidine kinase

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

8rjp__assembly_1__model_1

8rjp__assembly_1__model_1 | I(q)

8rjp__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (7)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 water

7. Citations (1)

Serial femtosecond X-ray structure of a fluorescence optimized bathy phytochrome PAiRFP2 derived from wild-type Agp2 in I2 intermediate state.

1. Protein Identity and Related Structures Protein Identity & Related Structures

histidine kinase

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

8rjp__assembly_1__model_1

8rjp__assembly_1__model_1 | I(q)

8rjp__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (7)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 water

7. Citations (1)