SAXSdb — 2bkx

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

GLUCOSAMINE-6-PHOSPHATE DEAMINASE

BACILLUS SUBTILIS

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	FRUCTOSE -6-PHOSPHATE × 1 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	FRUCTOSE -6-PHOSPHATE × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	NAGB_BACSU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–242； UniProt 1–242 Author chain B； PDBConstruct 1–242； UniProt 1–242

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	2bkx
Deposition date deposition_date	2005-02-21
Structure title title	Structure and kinetics of a monomeric glucosamine-6-phosphate deaminase: missing link of the NagB superfamily
Keywords keywords	HYDROLASE, SUBSTRATE INHIBITION, FRUCTOSE-6-PHOSPHATE; 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.

2bkx__assembly_1__model_1

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

Download this curve (.dat)

2bkx__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2bkx__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	18.19 Å
Rg (electron density)	16.87 Å
Total Rg	17.88 Å
Atom count	1914
Residues	242
Excluded volume	33733 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2bkx__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2bkx__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 (3)

Entity 1 Entity 1 polymer

Description description	GLUCOSAMINE-6-PHOSPHATE DEAMINASE
Molecular weight formula_weight	27025.3 kDa
EC 编号 ec_number	3.5.99.6
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	4626

MKVMECQTYEELSQIAARITADTIKEKPDAVLGLATGGTPEGTYRQLIRLHQTENLSFQNITTVNLDEYAGLSSDDPNSYHFYMNDRFFQHIDSKPSRHFIPNGNADDLEAECRRYEQLVDSLGDTDIQLLGIGRNGHIGFNEPGTSFKSRTHVVTLNEQTRQANARYFPSIDSVPKKALTMGIQTILSSKRILLLISGKSKAEAVRKLLEGNISEDFPASALHLHSDVTVLIDREAASLRP

Source Source

Source organism organism	BACILLUS SUBTILIS
NCBI taxonomy ID ncbi_taxonomy_id	1423
Host organism host_organism	ESCHERICHIA COLI

Entity 2 Entity 2 non-polymer

Description description	FRUCTOSE -6-PHOSPHATE
Molecular weight formula_weight	260.1 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	730

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6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	2bkxA00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1360 —

Domain ID domain_id	2bkxB00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1360 —

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Unit-cell length a length_a	62.966 Å
Unit-cell length b length_b	47.898 Å
Unit-cell length c length_c	71.397 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.06 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

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

Resolution resolution	1.400 Å
Low-resolution limit resolution_low	70.710 Å
R factor r_factor	0.1220
R_work r_work	0.1190
R_free r_free	0.1650

Structure and kinetics of a monomeric glucosamine-6-phosphate deaminase: missing link of the NagB superfamily

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

GLUCOSAMINE-6-PHOSPHATE DEAMINASE

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

2bkx__assembly_1__model_1

2bkx__assembly_1__model_1 | I(q)

2bkx__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) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)

Structure and kinetics of a monomeric glucosamine-6-phosphate deaminase: missing link of the NagB superfamily

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

GLUCOSAMINE-6-PHOSPHATE DEAMINASE

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

2bkx__assembly_1__model_1

2bkx__assembly_1__model_1 | I(q)

2bkx__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) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)