SAXSdb — 3fhq

▼

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

Endo-beta-N-acetylglucosaminidase

Arthrobacter protophormiae

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Homooligomer	Protein 2 其他Polymer 2	alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose × 2 3AR,5R,6S,7R,7AR-5-HYDROXYMETHYL-2-METHYL-5,6,7,7A-TETRAHYDRO-3AH-PYRANO[3,2-D]THIAZOLE-6,7-DIOL × 2 water × 2	Consistent with protein count
2	Other combination	Homooligomer	Protein 2 其他Polymer 2	alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose × 2 3AR,5R,6S,7R,7AR-5-HYDROXYMETHYL-2-METHYL-5,6,7,7A-TETRAHYDRO-3AH-PYRANO[3,2-D]THIAZOLE-6,7-DIOL × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q9ZB22_9MICC
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–621； UniProt 25–645 Author chain B； PDBConstruct 1–621； UniProt 25–645 Author chain D； PDBConstruct 1–621； UniProt 25–645 Author chain F； PDBConstruct 1–621； UniProt 25–645

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	3fhq
Deposition date deposition_date	2008-12-10
Structure title title	Structure of endo-beta-N-acetylglucosaminidase A
Keywords keywords	Endo-A, glycoprotein, Man3GlcNAc-thiazoline, GlcNAc-Asn, Glycosidase, Hydrolase; HYDROLASE
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.

3fhq__assembly_1__model_1

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

Download this curve (.dat)

3fhq__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3fhq__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	32.34 Å
Rg (electron density)	31.08 Å
Total Rg	31.84 Å
Atom count	9632
Residues	1200
Excluded volume	167970 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3fhq__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3fhq__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Endo-beta-N-acetylglucosaminidase
Molecular weight formula_weight	69669.9 kDa
EC 编号 ec_number	3.2.1.96
Mutation mutation	N43D, G455D, I518T, L583I
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,D,F
Atom count atom_count	20045

STYNGPLSSHWFPEELAQWEPDSDPDAPFNRSHVPLEPGRVADRVNANADKDAHLVSLSALNRHTSGVPSQGAPVFYENTFSYWHYTDLMVYWAGSAGEGIIVPPSADVIDASHRNGVPILGNVFFPPTVYGGQLEWLEQMLEQEEDGSFPLADKLLEVADYYGFDGWFINQETEGADEGTAEAMQAFLVYLQEQKPEGMHIMWYDSMIDTGAIAWQNHLTDRNKMYLQNGSTRVADSMFLNFWWRDQRQSNELAQALGRSPYDLYAGVDVEARGTSTPVQWEGLFPEGEKAHTSLGLYRPDWAFQSSETMEAFYEKELQFWVGSTGNPAETDGQSNWPGMAHWFPAKSTATSVPFVTHFNTGSGAQFSAEGKTVSEQEWNNRSLQDVLPTWRWIQHGGDLEATFSWEEAFEGGSSLQWHGSLAEGEHAQIELYQTELPISEGTSLTWTFKSEHDNDLNVGFRLDGEEDFRYVEGEQRESINGWTQWTLPLDAFAGQTITGLAFAAEGNETGLAEFYTGQLAVGADSEKPAAPNVNVRQYDPDPSGIQLVWEKQSNVHHYRVYKETKHGKELIGTSAGDRIYIEGLVEESKQNDVRLHIEALSETFVPSDARMIDIKSGSF

Source Source

Source organism organism	Arthrobacter protophormiae
NCBI taxonomy ID ncbi_taxonomy_id	37930
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 branched

Description description	alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose
Molecular weight formula_weight	504.4 kDa
Source method src_method	man
Copy count entity_count	4

Entity 3 Entity 3 non-polymer

Description description	3AR,5R,6S,7R,7AR-5-HYDROXYMETHYL-2-METHYL-5,6,7,7A-TETRAHYDRO-3AH-PYRANO[3,2-D]THIAZOLE-6,7-DIOL
Molecular weight formula_weight	219.3 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	837

▼

6. Fold Classification (SCOP + CATH) 12 domains

CATH v4.4 (12 domains)

Domain ID domain_id	3fhqA01
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	3fhqA02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	260 — Galactose-binding domain-like

Domain ID domain_id	3fhqA03
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	3fhqB01
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	3fhqB02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	260 — Galactose-binding domain-like

Domain ID domain_id	3fhqB03
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	3fhqD01
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	3fhqD02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	260 — Galactose-binding domain-like

Domain ID domain_id	3fhqD03
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	3fhqF01
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	3fhqF02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	260 — Galactose-binding domain-like

Domain ID domain_id	3fhqF03
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

▶

Unit-cell length a length_a	78.328 Å
Unit-cell length b length_b	79.265 Å
Unit-cell length c length_c	117.043 Å
Unit-cell angle α angle_alpha	80.51 °
Unit-cell angle β angle_beta	83.84 °
Unit-cell angle γ angle_gamma	64.33 °
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	2.452 Å
Low-resolution limit resolution_low	35.409 Å
R factor r_factor	0.2228
R_work r_work	0.2206
R_free r_free	0.2637

Structure of endo-beta-N-acetylglucosaminidase A

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

Endo-beta-N-acetylglucosaminidase

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

3fhq__assembly_1__model_1

3fhq__assembly_1__model_1 | I(q)

3fhq__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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 branched

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 12 domains

CATH v4.4 (12 domains)

7. Citations (1)

Structure of endo-beta-N-acetylglucosaminidase A

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

Endo-beta-N-acetylglucosaminidase

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

3fhq__assembly_1__model_1

3fhq__assembly_1__model_1 | I(q)

3fhq__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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 branched

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 12 domains

CATH v4.4 (12 domains)

7. Citations (1)