SAXSdb — 3lk6

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

Lipoprotein ybbD

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	DI(HYDROXYETHYL)ETHER × 4 SODIUM ION × 1 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	DI(HYDROXYETHYL)ETHER × 6 SODIUM ION × 1 water × 1	Consistent with protein count
3	Protein monomer	Monomer	Protein 1	DI(HYDROXYETHYL)ETHER × 5 SODIUM ION × 1 water × 1	Consistent with protein count
4	Protein monomer	Monomer	Protein 1	DI(HYDROXYETHYL)ETHER × 4 SODIUM ION × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	YBBD_BACSU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–616； UniProt 27–642 Author chain B； PDBConstruct 1–616； UniProt 27–642 Author chain C； PDBConstruct 1–616； UniProt 27–642 Author chain D； PDBConstruct 1–616； UniProt 27–642

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	3lk6
Deposition date deposition_date	2010-01-27
Structure title title	Beta-N-hexosaminidase N318D mutant (YBBD_N318D) from bacillus subtilis
Keywords keywords	bacillus subtilis, hexosaminidase, Cell membrane, Glycosidase, Hydrolase, Lipoprotein, Membrane, Palmitate; 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.

3lk6__assembly_3__model_1

Assembly 3 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

3lk6__assembly_3__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3lk6__assembly_3__model_1 | P(r) · Pending

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

Rg（Guinier）	26.95 Å
Rg (electron density)	26.03 Å
Total Rg	26.94 Å
Atom count	4844
Residues	616
Excluded volume	86117 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3lk6__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3lk6__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`3lk6__assembly_3__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`3lk6__assembly_4__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 (4)

Entity 1 Entity 1 polymer

Description description	Lipoprotein ybbD
Molecular weight formula_weight	67774.8 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	19416

SASKRAIDANQIVNRMSLDEKLGQMLMPDFRNWQKEGESSPQALTKMNDEVASLVKKYQFGGIILFAENVKTTKQTVQLTDDYQKASPKIPLMLSIDQEGGIVTRLGEGTNFPGNMALGAARSRINAYQTGSIIGKELSALGINTDFSPVVDINNNPDNPVIGVRSFSSNRELTSRLGLYTMKGLQRQDIASALKHFPGHGDTDVDSHYGLPLVSHGQERLREVELYPFQKAIDAGADMVMTAHVQFPAFDDTTYKSKLDGSDILVPATLSKKVMTGLLRQEMGFNGVIVTNALNMKAIADHFGQEEAVVMAVKAGVDIALMPASVTSLKEEQKFARVIQALKEAVKNGDIPEQQINNSVERIISLKIKRGMYPARNSDSTKEKIAKAKKIVGSKQHLKAEKKLAEKAVTVLKNEQHTLPFKPKKGSRILIVAPYEEQTASIEQTIHDLIKRKKIKPVSLSKMNFASQVFKTEHEKQVKEADYIITGSYVVKNDPVVNDGVIDDTISDSSKWATVFPRAVMKAALQHNKPFVLMSLRNPYDAANFEEAKALIAVYGFKGYANGRYLQPNIPAGVMAIFGQAKPKGTLPVDIPSVTKPGNTLYPLGYGLNIKTGRPL

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	DI(HYDROXYETHYL)ETHER
Molecular weight formula_weight	106.1 kDa
Source method src_method	syn
Copy count entity_count	19

Entity 3 Entity 3 non-polymer

Description description	SODIUM ION
Molecular weight formula_weight	23.0 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	75

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6. Fold Classification (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

Domain ID domain_id	3lk6A01
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	300 — Glycoside hydrolase, family 3, N-terminal domain

Domain ID domain_id	3lk6A02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1700 — Glycoside hydrolase family 3 C-terminal domain

Domain ID domain_id	3lk6B01
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	300 — Glycoside hydrolase, family 3, N-terminal domain

Domain ID domain_id	3lk6B02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1700 — Glycoside hydrolase family 3 C-terminal domain

Domain ID domain_id	3lk6C01
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	300 — Glycoside hydrolase, family 3, N-terminal domain

Domain ID domain_id	3lk6C02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1700 — Glycoside hydrolase family 3 C-terminal domain

Domain ID domain_id	3lk6D01
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	300 — Glycoside hydrolase, family 3, N-terminal domain

Domain ID domain_id	3lk6D02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1700 — Glycoside hydrolase family 3 C-terminal domain

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Unit-cell length a length_a	56.315 Å
Unit-cell length b length_b	99.149 Å
Unit-cell length c length_c	139.861 Å
Unit-cell angle α angle_alpha	90.11 °
Unit-cell angle β angle_beta	90.05 °
Unit-cell angle γ angle_gamma	89.94 °
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	2.880 Å
Low-resolution limit resolution_low	48.988 Å
R factor r_factor	0.1728
R_work r_work	0.1713
R_free r_free	0.2006

Beta-N-hexosaminidase N318D mutant (YBBD_N318D) from bacillus subtilis

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

Lipoprotein ybbD

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

3lk6__assembly_3__model_1

3lk6__assembly_3__model_1 | I(q)

3lk6__assembly_3__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 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

7. Citations (1)

Beta-N-hexosaminidase N318D mutant (YBBD_N318D) from bacillus subtilis

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

Lipoprotein ybbD

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

3lk6__assembly_3__model_1

3lk6__assembly_3__model_1 | I(q)

3lk6__assembly_3__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 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

7. Citations (1)