SAXSdb — 1m03

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

Beta-N-acetylhexosaminidase

Streptomyces plicatus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	2-acetamido-2-deoxy-beta-D-glucopyranose × 1 CHLORIDE ION × 3 SULFATE ION × 1 GLYCEROL × 2 water × 1	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 2	2-acetamido-2-deoxy-beta-D-glucopyranose × 2 CHLORIDE ION × 6 SULFATE ION × 2 GLYCEROL × 4 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	O85361_STRPL
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 9–512； UniProt 3–506

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	1m03
Deposition date deposition_date	2002-06-11
Structure title title	Mutant Streptomyces plicatus beta-hexosaminidase (D313A) in complex with product (GlcNAc)
Keywords keywords	substrate assisted catalysis, family 20 glycosidase, beta-hexosaminidase, 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.

1m03__assembly_2__model_1

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

Download this curve (.dat)

1m03__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1m03__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	33.82 Å
Rg (electron density)	33.54 Å
Total Rg	33.93 Å
Atom count	7791
Residues	998
Excluded volume	137460 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1m03__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1m03__assembly_2__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 (6)

Entity 1 Entity 1 polymer

Description description	Beta-N-acetylhexosaminidase
Molecular weight formula_weight	56082.8 kDa
EC 编号 ec_number	3.2.1.52
Mutation mutation	D319A
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	4206

MHHHHHHHTGAAPDRKAPVRPTPLDRVIPAPASVDPGGAPYRITRGTHIRVDDSREARRVGDYLADLLRPATGYRLPVTAHGHGGIRLRLAGGPYGDEGYRLDSGPAGVTITARKAAGLFHGVQTLRQLLPPAVEKDSAQPGPWLVAGGTIEDTPRYAWRSAMLDVSRHFFGVDEVKRYIDRVARYKYNKLHLHLSDDQGWRIAIDSWPRLATYGGSTEVGGGPGGYYTKAEYKEIVRYAASRHLEVVPEIDMPGHTNAALASYAELNCDGVAPPLYTGTKVGFSSLCVDKDVTYDFVDDVIGELAALTPGRYLHIGGAEAHSTPKADFVAFMKRVQPIVAKYGKTVVGWHQLAGAEPVEGALVQYWGLDRTGDAEKAEVAEAARNGTGLILSPADRTYLDMKYTKDTPLGLSWAGYVEVQRSYDWDPAGYLPGAPADAVRGVEAPLWTETLSDPDQLDYMAFPRLPGVAELGWSPASTHDWDTYKVRLAAQAPYWEAAGIDFYRSPQVPWT

Source Source

Source organism organism	Streptomyces plicatus
NCBI taxonomy ID ncbi_taxonomy_id	1922
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	221.2 kDa
Source method src_method	man
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 4 Entity 4 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 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	295

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6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1m03a1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.8 — (Trans)glycosidases
Family Family family	c.1.8.6 — beta-N-acetylhexosaminidase catalytic domain

Domain ID domain_id	d1m03a2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.92 — Zincin-like
Superfamily Superfamily superfamily	d.92.2 — beta-N-acetylhexosaminidase-like domain
Family Family family	d.92.2.1 — beta-N-acetylhexosaminidase domain

CATH v4.4 (2 domains)

Domain ID domain_id	1m03A01
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	80 — Glycosidases

Domain ID domain_id	1m03A02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	379 — Chitobiase; domain 2
Homologous superfamily homologous superfamily	10 — Chitobiase/beta-hexosaminidase domain 2-like

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Unit-cell length a length_a	132.903 Å
Unit-cell length b length_b	132.903 Å
Unit-cell length c length_c	176.944 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	12

Space group space_group	P 61 2 2
Space-group number int_tables_number	178
Crystal system crystal_system	—

Resolution resolution	1.900 Å
Low-resolution limit resolution_low	38.370 Å
R factor r_factor	0.1940
R_work r_work	0.1940
R_free r_free	0.2140

Mutant Streptomyces plicatus beta-hexosaminidase (D313A) in complex with product (GlcNAc)

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

Beta-N-acetylhexosaminidase

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

1m03__assembly_2__model_1

1m03__assembly_2__model_1 | I(q)

1m03__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 (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) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)

Mutant Streptomyces plicatus beta-hexosaminidase (D313A) in complex with product (GlcNAc)

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

Beta-N-acetylhexosaminidase

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

1m03__assembly_2__model_1

1m03__assembly_2__model_1 | I(q)

1m03__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 (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) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)