3mzi

Crystallographic structure of the pseudo-Signaling State of the BLUF Photoreceptor PixD (slr1694) Y8F mutant

Method: X-RAY DIFFRACTION

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

Activator of photopigment and puc expression

Synechocystis sp. PCC 6803

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	FLAVIN MONONUCLEOTIDE × 2 water × 2	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 2	FLAVIN MONONUCLEOTIDE × 2 water × 2	Consistent with protein count
3	Protein homooligomer	Homooligomer	Protein 2	FLAVIN MONONUCLEOTIDE × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	P74295_SYNY3
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–150； UniProt 1–150 Author chain B； PDBConstruct 1–150； UniProt 1–150 Author chain C； PDBConstruct 1–150； UniProt 1–150 Author chain D； PDBConstruct 1–150； UniProt 1–150 Author chain E； PDBConstruct 1–150； UniProt 1–150 Author chain F； PDBConstruct 1–150； UniProt 1–150

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	3mzi
Deposition date deposition_date	2010-05-12
Structure title title	Crystallographic structure of the pseudo-Signaling State of the BLUF Photoreceptor PixD (slr1694) Y8F mutant
Keywords keywords	BLUF (blue-light using FAD) domain, signaling state, phototaxis, protein binding; PROTEIN BINDING
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.

3mzi__assembly_1__model_1

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

Download this curve (.dat)

3mzi__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3mzi__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	20.83 Å
Rg (electron density)	20.19 Å
Total Rg	21.00 Å
Atom count	2324
Residues	280
Excluded volume	41211 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3mzi__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3mzi__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`3mzi__assembly_3__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 (3)

Entity 1 Entity 1 polymer

Description description	Activator of photopigment and puc expression
Molecular weight formula_weight	17341.7 kDa
Mutation mutation	Y8F
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F
Atom count atom_count	7061

MSLYRLIFSSQGIPNLQPQDLKDILESSQRNNPANGITGLLCYSKPAFLQVLEGECEQVNETYHRIVQDERHHSPQIIECMPIRRRNFEVWSMQAITVNDLSTEQVKTLVLKYSGFTTLRPSAMDPEQCLNFLLDIAKIYELSDNFFLDL

Source Source

Source organism organism	Synechocystis sp. PCC 6803
NCBI taxonomy ID ncbi_taxonomy_id	1148
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	FLAVIN MONONUCLEOTIDE
Molecular weight formula_weight	456.3 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	89

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6. Fold Classification (SCOP + CATH) 18 domains

SCOP 2.08 (6 domains)

Domain ID domain_id	d3mzia_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.58 — Ferredoxin-like
Superfamily Superfamily superfamily	d.58.10 — Acylphosphatase/BLUF domain-like
Family Family family	d.58.10.0 — automated matches

Domain ID domain_id	d3mzib_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.58 — Ferredoxin-like
Superfamily Superfamily superfamily	d.58.10 — Acylphosphatase/BLUF domain-like
Family Family family	d.58.10.0 — automated matches

Domain ID domain_id	d3mzic_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.58 — Ferredoxin-like
Superfamily Superfamily superfamily	d.58.10 — Acylphosphatase/BLUF domain-like
Family Family family	d.58.10.0 — automated matches

Domain ID domain_id	d3mzid_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.58 — Ferredoxin-like
Superfamily Superfamily superfamily	d.58.10 — Acylphosphatase/BLUF domain-like
Family Family family	d.58.10.0 — automated matches

Domain ID domain_id	d3mzie_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.58 — Ferredoxin-like
Superfamily Superfamily superfamily	d.58.10 — Acylphosphatase/BLUF domain-like
Family Family family	d.58.10.0 — automated matches

Domain ID domain_id	d3mzif_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.58 — Ferredoxin-like
Superfamily Superfamily superfamily	d.58.10 — Acylphosphatase/BLUF domain-like
Family Family family	d.58.10.0 — automated matches

CATH v4.4 (12 domains)

Domain ID domain_id	3mziA01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	100 —

Domain ID domain_id	3mziA02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	287 — Helix Hairpins
Homologous superfamily homologous superfamily	1540 —

Domain ID domain_id	3mziB01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	100 —

Domain ID domain_id	3mziB02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	287 — Helix Hairpins
Homologous superfamily homologous superfamily	1540 —

Domain ID domain_id	3mziC01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	100 —

Domain ID domain_id	3mziC02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	287 — Helix Hairpins
Homologous superfamily homologous superfamily	1540 —

Domain ID domain_id	3mziD01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	100 —

Domain ID domain_id	3mziD02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	287 — Helix Hairpins
Homologous superfamily homologous superfamily	1540 —

Domain ID domain_id	3mziE01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	100 —

Domain ID domain_id	3mziE02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	287 — Helix Hairpins
Homologous superfamily homologous superfamily	1540 —

Domain ID domain_id	3mziF01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	100 —

Domain ID domain_id	3mziF02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	287 — Helix Hairpins
Homologous superfamily homologous superfamily	1540 —

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Unit-cell length a length_a	41.850 Å
Unit-cell length b length_b	119.480 Å
Unit-cell length c length_c	93.260 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	102.89 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	12

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	2.304 Å
Low-resolution limit resolution_low	49.925 Å
R factor r_factor	0.1665
R_work r_work	0.1645
R_free r_free	0.2155

Crystallographic structure of the pseudo-Signaling State of the BLUF Photoreceptor PixD (slr1694) Y8F mutant

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

Activator of photopigment and puc expression

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

3mzi__assembly_1__model_1

3mzi__assembly_1__model_1 | I(q)

3mzi__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 18 domains

SCOP 2.08 (6 domains)

CATH v4.4 (12 domains)

7. Citations (1)

Crystallographic structure of the pseudo-Signaling State of the BLUF Photoreceptor PixD (slr1694) Y8F mutant

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

Activator of photopigment and puc expression

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

3mzi__assembly_1__model_1

3mzi__assembly_1__model_1 | I(q)

3mzi__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 18 domains

SCOP 2.08 (6 domains)

CATH v4.4 (12 domains)

7. Citations (1)