SAXSdb — 3brm

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

Glutaminase 1

Bacillus subtilis

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	5-OXO-L-NORLEUCINE × 2 water × 2	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 4	5-OXO-L-NORLEUCINE × 4 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	GLSA1_BACSU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–330； UniProt 1–327 Author chain B； PDBConstruct 4–330； UniProt 1–327

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	3brm
Deposition date deposition_date	2007-12-21
Structure title title	Crystal structure of the covalent complex between the Bacillus subtilis glutaminase YbgJ and 5-oxo-L-norleucine formed by reaction of the protein with 6-diazo-5-oxo-L-norleucine
Keywords keywords	covalent complex, YbaS glutaminase, DON, Hydrolase; HYDROLASE
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.

3brm__assembly_2__model_1

Assembly 2 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

3brm__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3brm__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	35.59 Å
Rg (electron density)	34.74 Å
Total Rg	35.21 Å
Atom count	9028
Residues	1120
Excluded volume	162250 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3brm__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3brm__assembly_2__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 (3)

Entity 1 Entity 1 polymer

Description description	Glutaminase 1
Molecular weight formula_weight	37059.5 kDa
EC 编号 ec_number	3.5.1.2
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	4815

SNAMKELIKEHQKDINPALQLHDWVEYYRPFAANGQSANYIPALGKVNDSQLGICVLEPDGTMIHAGDWNVSFTMQSISKVISFIAACMSRGIPYVLDRVDVEPTGDAFNSIIRLEINKPGKPFNPMINAGALTIASILPGESAYEKLEFLYSVMETLIGKRPRIHEEVFRSEWETAHRNRALAYYLKETNFLEAEVEETLEVYLKQCAMESTTEDIALIGLILAHDGYHPIRHEQVIPKDVAKLAKALMLTCGMYNASGKYAAFVGVPAKSGVSGGIMALVPPSARREQPFQSGCGIGIYGPAIDEYGNSLTGGMLLKHMAQEWELSIF

Source Source

Source organism organism	Bacillus subtilis
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	5-OXO-L-NORLEUCINE
Molecular weight formula_weight	145.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	295

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6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d3brma_
Class class	e — Multi-domain proteins (alpha and beta)
Fold Fold fold	e.3 — beta-lactamase/transpeptidase-like
Superfamily Superfamily superfamily	e.3.1 — beta-lactamase/transpeptidase-like
Family Family family	e.3.1.2 — Glutaminase

Domain ID domain_id	d3brmb_
Class class	e — Multi-domain proteins (alpha and beta)
Fold Fold fold	e.3 — beta-lactamase/transpeptidase-like
Superfamily Superfamily superfamily	e.3.1 — beta-lactamase/transpeptidase-like
Family Family family	e.3.1.2 — Glutaminase

CATH v4.4 (4 domains)

Domain ID domain_id	3brmA01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	710 — Beta-lactamase
Homologous superfamily homologous superfamily	10 — DD-peptidase/beta-lactamase superfamily

Domain ID domain_id	3brmA02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1500 — Probable Glutaminase Ybgj; Chain: A, domain 2
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	3brmB01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	710 — Beta-lactamase
Homologous superfamily homologous superfamily	10 — DD-peptidase/beta-lactamase superfamily

Domain ID domain_id	3brmB02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1500 — Probable Glutaminase Ybgj; Chain: A, domain 2
Homologous superfamily homologous superfamily	10 —

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Unit-cell length a length_a	71.247 Å
Unit-cell length b length_b	184.701 Å
Unit-cell length c length_c	51.422 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 21 21 2
Space-group number int_tables_number	18
Crystal system crystal_system	—

Resolution resolution	2.290 Å
Low-resolution limit resolution_low	34.520 Å
R factor r_factor	0.1781
R_work r_work	0.1744
R_free r_free	0.2481

Crystal structure of the covalent complex between the Bacillus subtilis glutaminase YbgJ and 5-oxo-L-norleucine formed by reaction of the protein with 6-diazo-5-oxo-L-norleucine

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

Glutaminase 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

3brm__assembly_2__model_1

3brm__assembly_2__model_1 | I(q)

3brm__assembly_2__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) 6 domains

SCOP 2.08 (2 domains)

CATH v4.4 (4 domains)

7. Citations (1)

Crystal structure of the covalent complex between the Bacillus subtilis glutaminase YbgJ and 5-oxo-L-norleucine formed by reaction of the protein with 6-diazo-5-oxo-L-norleucine

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

Glutaminase 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

3brm__assembly_2__model_1

3brm__assembly_2__model_1 | I(q)

3brm__assembly_2__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) 6 domains

SCOP 2.08 (2 domains)

CATH v4.4 (4 domains)

7. Citations (1)