SAXSdb — 5ovo

▼

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

ADP-ribosyl-(Dinitrogen reductase) hydrolase

Azospirillum brasilense

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 6	Nitrogen regulatory protein P-II 1 × 3 （P70731） ADENOSINE-5'-DIPHOSPHATE × 6 MAGNESIUM ION × 6 MANGANESE (II) ION × 3 water × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A7XNI2_AZOBR
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–297； UniProt 1–297

Nitrogen regulatory protein P-II 1

Azospirillum brasilense

UniProt P70731

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 6	ADP-ribosyl-(Dinitrogen reductase) hydrolase × 3 （A7XNI2） ADENOSINE-5'-DIPHOSPHATE × 6 MAGNESIUM ION × 6 MANGANESE (II) ION × 3 water × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	P70731_AZOBR
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–99； UniProt 1–112

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	5ovo
Deposition date deposition_date	2017-08-29
Structure title title	Structure of DraG-GlnZ-delta42-54 complex from Azospirillum brasilense
Keywords keywords	Glycohydrolase, METAL BINDING PROTEIN; METAL BINDING PROTEIN
Experimental Method method	X-RAY DIFFRACTION

▼

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.

5ovo__assembly_1__model_1

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

Download this curve (.dat)

5ovo__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5ovo__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	40.42 Å
Rg (electron density)	40.26 Å
Total Rg	40.24 Å
Atom count	9228
Residues	1182
Excluded volume	163130 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5ovo__assembly_1__model_1`	hexameric （6）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Description description	ADP-ribosyl-(Dinitrogen reductase) hydrolase
Molecular weight formula_weight	32442.8 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	3637

MTDHSIRSRALGAYLGLACGDALGATVEFLTKGEIAHQYGVHKHIKGGGWLKLPAGQVTDDTEMSIHLGRAILAAPEWDARRAAEEFAVWLKGVPVDVGDTTRRGIRRFIMHGTLSEPESEYHAGNGAAMRNLPVALATLGDDAAFERWTVEQAHITHCNAMSDAATLTLGHMVRRLVLGGDVRDVRDESNKLIAKHRQFKFQPYRGLATAYIVDTMQTVMHYYFQTDSVESCVVETVNQGGDADTTGAIAGMLAGATYGVETIPPRWLRKLDRDVYNEICAQVDGLLARAPALKQG

Source Source

Source organism organism	Azospirillum brasilense
NCBI taxonomy ID ncbi_taxonomy_id	192
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Nitrogen regulatory protein P-II 1
Molecular weight formula_weight	10801.5 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

MKLVMAIIKPFKLDEVREALTSLGIQGLTVSEVKGFGRQKGFLPKVKVEVAVSDDQYEQVVEAIQKAANTGRIGDGKIFVLDIAQAVRIRTGETNTEAL

Source Source

Source organism organism	Azospirillum brasilense
NCBI taxonomy ID ncbi_taxonomy_id	192
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 non-polymer

Description description	ADENOSINE-5'-DIPHOSPHATE
Molecular weight formula_weight	427.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 non-polymer

Description description	MANGANESE (II) ION
Molecular weight formula_weight	54.9 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	507

▼

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d5ovoa_
Class class	a — All alpha proteins
Fold Fold fold	a.209 — ADP-ribosylglycohydrolase
Superfamily Superfamily superfamily	a.209.1 — ADP-ribosylglycohydrolase
Family Family family	a.209.1.0 — automated matches

Domain ID domain_id	d5ovob_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.58 — Ferredoxin-like
Superfamily Superfamily superfamily	d.58.5 — GlnB-like
Family Family family	d.58.5.1 — Prokaryotic signal transducing protein

CATH v4.4 (2 domains)

Domain ID domain_id	5ovoA00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	4080 — ADP-ribosylglycohydrolase fold
Homologous superfamily homologous superfamily	10 — ADP-ribosylation/Crystallin J1

Domain ID domain_id	5ovoB00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	120 —

▶

Unit-cell length a length_a	116.740 Å
Unit-cell length b length_b	116.740 Å
Unit-cell length c length_c	105.616 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	9

Space group space_group	H 3
Space-group number int_tables_number	146
Crystal system crystal_system	—

Resolution resolution	1.550 Å
Low-resolution limit resolution_low	45.600 Å
R factor r_factor	0.1451
R_work r_work	0.1440
R_free r_free	0.1645

Structure of DraG-GlnZ-delta42-54 complex from Azospirillum brasilense

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

ADP-ribosyl-(Dinitrogen reductase) hydrolase

State in the Current Structure

Other States of the Same Protein in the Database

Nitrogen regulatory protein P-II 1

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

5ovo__assembly_1__model_1

5ovo__assembly_1__model_1 | I(q)

5ovo__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 polymer

Polymer Polymer

Source Source

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) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)

Structure of DraG-GlnZ-delta42-54 complex from Azospirillum brasilense

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

ADP-ribosyl-(Dinitrogen reductase) hydrolase

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Nitrogen regulatory protein P-II 1

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

5ovo__assembly_1__model_1

5ovo__assembly_1__model_1 | I(q)

5ovo__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 polymer

Polymer Polymer

Source Source

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) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)