6g1z

Crystal structure of a fluorescence optimized bathy phytochrome PAiRFP2 derived from wild-type Agp2 in its Pfr state.

Method: X-RAY DIFFRACTION

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

Bacteriophytochrome protein

Agrobacterium fabrum (strain C58 / ATCC 33970)

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	;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 ; × 1 SULFATE ION × 6 GLYCEROL × 2 DI(HYDROXYETHYL)ETHER × 1 2-{2-[2-2-(METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL × 1 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	;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 ; × 1 SULFATE ION × 8 GLYCEROL × 5 DI(HYDROXYETHYL)ETHER × 1 2-{2-[2-2-(METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL × 1 2-(2-METHOXYETHOXY)ETHANOL × 1 water × 1	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 1–505； UniProt 1–505 Author chain B； PDBConstruct 1–505； UniProt 1–505

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	6g1z
Deposition date deposition_date	2018-03-22
Structure title title	Crystal structure of a fluorescence optimized bathy phytochrome PAiRFP2 derived from wild-type Agp2 in its Pfr state.
Keywords keywords	;FLUORESCENT PROTEIN, SIGNALING PROTEIN, PHYTOCHROME, BACTERIOPHYTOCHROME, BILIN CHROMOPHORE, PHOTOISOMERIZATION, SIGNAL TRANSDUCTION, PFR-STATE, LIGHT ADAPTATION, BATHY PHYTOCHROME, PHOTOSENSORY CORE MODULE, OPTOGENETIC, FLOURESCENCE ;; FLUORESCENT 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.

6g1z__assembly_1__model_1

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

Download this curve (.dat)

6g1z__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6g1z__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	29.25 Å
Rg (electron density)	28.52 Å
Total Rg	29.09 Å
Atom count	3881
Residues	489
Excluded volume	68732 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6g1z__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`6g1z__assembly_2__model_1`	monomeric （1）	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 (8)

Entity 1 Entity 1 polymer

Description description	Bacteriophytochrome protein
Molecular weight formula_weight	56678.6 kDa
EC 编号 ec_number	2.7.13.3
Mutation mutation	YES
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	8847

MASTDYHVDLTNCDREPIHIPGYIQPHGCLIACDNAMRMVLRHSENCGELLGLEGDLNGRTAEDVLGKRLVHDLRNALTVTGKTTRPAMLPAMETSDGRSFDISLHRYKSTTIIEFEPSDSDTQPLGTARKMVDRIREADSVESLISRTTRLVKATLGYDRVLIYRFEEDGAGKVVSEAKQPELESFLGQYFPASDIPQQARALYLKNTLRIISDASGTPIPVLPAVDVSGEPLDLSYAHLRNFSPIHCEYLRNMGVAASMSISVIVDDALWGLIVCHHCSPRVLSMPVRIAAAMFGEFFSMFLQVLKQKRRLDTINHAHAALDRFLRLAAHRANLEELLVDSFQDFARLIPCDGVGLWVGNNWHGHGATPPHDAIPRLARFVASVSEGRVWATHALSQAIPEAEIYADTAAGMLAIPISQVKSDYLLFFRKEIVQNLNWAGNPEKSYETGPMGDRLTPRKSFAIWKESVRLQAQPWSEADREIAETARIALVGVAFHHSELMAGLEYK

Source Source

Source organism organism	Agrobacterium fabrum (strain C58 / ATCC 33970)
Common name common_name	Agrobacterium tumefaciens
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	14

Entity 4 Entity 4 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	7

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	2-{2-[2-2-(METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL
Molecular weight formula_weight	208.3 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 7 Entity 7 non-polymer

Description description	2-(2-METHOXYETHOXY)ETHANOL
Molecular weight formula_weight	120.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 8 Entity 8 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	853

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6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id	6g1zA01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	450 — Beta-Lactamase
Homologous superfamily homologous superfamily	40 — GAF domain

Domain ID domain_id	6g1zA02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	450 — Beta-Lactamase
Homologous superfamily homologous superfamily	20 — PAS domain

Domain ID domain_id	6g1zB01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	450 — Beta-Lactamase
Homologous superfamily homologous superfamily	40 — GAF domain

Domain ID domain_id	6g1zB02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	450 — Beta-Lactamase
Homologous superfamily homologous superfamily	20 — PAS domain

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Unit-cell length a length_a	182.377 Å
Unit-cell length b length_b	182.377 Å
Unit-cell length c length_c	179.883 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	2.030 Å
Low-resolution limit resolution_low	47.730 Å
R factor r_factor	0.1820
R_work r_work	0.1800
R_free r_free	0.2130

Crystal structure of a fluorescence optimized bathy phytochrome PAiRFP2 derived from wild-type Agp2 in its Pfr state.

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

Bacteriophytochrome protein

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

6g1z__assembly_1__model_1

6g1z__assembly_1__model_1 | I(q)

6g1z__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 (8)

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 non-polymer

Entity 8 Entity 8 water

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)

Crystal structure of a fluorescence optimized bathy phytochrome PAiRFP2 derived from wild-type Agp2 in its Pfr state.

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

Bacteriophytochrome protein

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

6g1z__assembly_1__model_1

6g1z__assembly_1__model_1 | I(q)

6g1z__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 (8)

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 non-polymer

Entity 8 Entity 8 water

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)