SAXSdb — 2vv8

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

SENSOR PROTEIN FIXL

BRADYRHIZOBIUM JAPONICUM

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 4	PROTOPORPHYRIN IX CONTAINING FE × 4 CARBON MONOXIDE × 4 SODIUM ION × 1 CHLORIDE ION × 2 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	FIXL_BRAJA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–119； UniProt 151–269 Author chain B； PDBConstruct 1–119； UniProt 151–269 Author chain C； PDBConstruct 1–119； UniProt 151–269 Author chain D； PDBConstruct 1–119； UniProt 151–269

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	2vv8
Deposition date deposition_date	2008-06-04
Structure title title	Co-bound structure of bjFixLH
Keywords keywords	SIGNALING PROTEIN, TRANSFERASE, PHOSPHOPROTEIN, NITROGEN FIXATION, PER-ARNT-SIM, PAS, KINASE, TWO-COMPONENT REGULATORY SYSTEM; 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.

2vv8__assembly_1__model_1

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

Download this curve (.dat)

2vv8__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2vv8__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	26.24 Å
Rg (electron density)	25.46 Å
Total Rg	26.13 Å
Atom count	3513
Residues	427
Excluded volume	62204 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2vv8__assembly_1__model_1`	tetrameric （4）	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 (6)

Entity 1 Entity 1 polymer

Description description	SENSOR PROTEIN FIXL
Molecular weight formula_weight	13413.1 kDa
EC 编号 ec_number	2.7.13.3, 2.7.3.-
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	4190

TIPDAMIVIDGHGIIQLFSTAAERLFGWSELEAIGQNVNILMPEPDRSRHDSYISRYRTTSDPHIIGIGRIVTGKRRDGTTFPMHLSIGEMQSGGEPYFTGFVRDLTEHQQTQARLQEL

Source Source

Source organism organism	BRADYRHIZOBIUM JAPONICUM
NCBI taxonomy ID ncbi_taxonomy_id	375
Host organism host_organism	ESCHERICHIA COLI

Entity 2 Entity 2 non-polymer

Description description	PROTOPORPHYRIN IX CONTAINING FE
Molecular weight formula_weight	616.5 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 non-polymer

Description description	CARBON MONOXIDE
Molecular weight formula_weight	28.0 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 4 Entity 4 non-polymer

Description description	SODIUM ION
Molecular weight formula_weight	23.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	468

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6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d2vv8a_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.110 — Profilin-like
Superfamily Superfamily superfamily	d.110.3 — PYP-like sensor domain (PAS domain)
Family Family family	d.110.3.2 — Heme-binding PAS domain

Domain ID domain_id	d2vv8b_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.110 — Profilin-like
Superfamily Superfamily superfamily	d.110.3 — PYP-like sensor domain (PAS domain)
Family Family family	d.110.3.2 — Heme-binding PAS domain

Domain ID domain_id	d2vv8c_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.110 — Profilin-like
Superfamily Superfamily superfamily	d.110.3 — PYP-like sensor domain (PAS domain)
Family Family family	d.110.3.2 — Heme-binding PAS domain

Domain ID domain_id	d2vv8d_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.110 — Profilin-like
Superfamily Superfamily superfamily	d.110.3 — PYP-like sensor domain (PAS domain)
Family Family family	d.110.3.2 — Heme-binding PAS domain

CATH v4.4 (4 domains)

Domain ID domain_id	2vv8A00
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	2vv8B00
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	2vv8C00
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	2vv8D00
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	48.923 Å
Unit-cell length b length_b	50.296 Å
Unit-cell length c length_c	58.993 Å
Unit-cell angle α angle_alpha	73.37 °
Unit-cell angle β angle_beta	70.26 °
Unit-cell angle γ angle_gamma	72.13 °
Molecules per unit cell Z z_pdb	4

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

Resolution resolution	1.610 Å
Low-resolution limit resolution_low	46.880 Å
R factor r_factor	0.2080
R_work r_work	0.2060
R_free r_free	0.2490

Co-bound structure of bjFixLH

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

SENSOR PROTEIN FIXL

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

2vv8__assembly_1__model_1

2vv8__assembly_1__model_1 | I(q)

2vv8__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 (6)

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 water

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)

Co-bound structure of bjFixLH

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

SENSOR PROTEIN FIXL

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

2vv8__assembly_1__model_1

2vv8__assembly_1__model_1 | I(q)

2vv8__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 (6)

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 water

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)