3fef

Crystal structure of putative glucosidase lplD from bacillus subtilis

Method: X-RAY DIFFRACTION

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

Putative glucosidase lplD, ALPHA-GALACTURONIDASE

Bacillus subtilis

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 4	SULFATE ION × 7 MAGNESIUM ION × 4 water × 4	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 2	SULFATE ION × 3 MAGNESIUM ION × 2 water × 2	Consistent with protein count
3	Protein homooligomer	Homooligomer	Protein 2	SULFATE ION × 4 MAGNESIUM ION × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	LPLD_BACSU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–442； UniProt 7–446 Author chain B； PDBConstruct 3–442； UniProt 7–446 Author chain C； PDBConstruct 3–442； UniProt 7–446 Author chain D； PDBConstruct 3–442； UniProt 7–446

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	3fef
Deposition date deposition_date	2008-11-28
Structure title title	Crystal structure of putative glucosidase lplD from bacillus subtilis
Keywords keywords	;lplD, gulosidase, structural genomics, UNKNOWN FUNCTION, Glycosidase, Hydrolase, Manganese, Metal-binding, NAD, PSI-2, Protein Structure Initiative, New York SGX Research Center for Structural Genomics, NYSGXRC ;; 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.

3fef__assembly_2__model_1

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

Download this curve (.dat)

3fef__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3fef__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	32.06 Å
Rg (electron density)	31.39 Å
Total Rg	31.86 Å
Atom count	6782
Residues	852
Excluded volume	120790 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3fef__assembly_1__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3fef__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`3fef__assembly_3__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 (4)

Entity 1 Entity 1 polymer

Description description	Putative glucosidase lplD, ALPHA-GALACTURONIDASE
Molecular weight formula_weight	50524.8 kDa
EC 编号 ec_number	3.2.1.67
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	14117

MSLDQIKIAYIGGGSQGWARSLMSDLSIDERMSGTVALYDLDFEAAQKNEVIGNHSGNGRWRYEAVSTLKKALSAADIVIISILPGSLDDMEVDVHLPERCGIYQSVGDTVGPGGIIRGLRAVPIFAEIARAIRDYAPESWVINYTNPMSVCTRVLYKVFPGIKAIGCCHEVFGTQKLLAEMVTERLGIEVPRREDIRVNVLGINHFTWITKASYRHIDLLPIFREFSAHYGESGYELEGECWRDSVFCSAHRVAFDLFETYGAIPAAGDRHLAEFLPGPYLKQPEVWKFHLTPISFRKQDRAEKRQETERLIVQQRGVAEKASGEEGVNIIAALLGLGELVTNVNMPNQGQVLNLPIQAIVETNAFITRNRVQPILSGALPKGVEMLAARHISNQEAVADAGLTKDTGLAFQAFLNDPLVQIDRSDAEQLFNDMLQCIMQSEGHHHHHH

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	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	7

Entity 3 Entity 3 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 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	535

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6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (8 domains)

Domain ID domain_id	d3fefa1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.2 — NAD(P)-binding Rossmann-fold domains
Superfamily Superfamily superfamily	c.2.1 — NAD(P)-binding Rossmann-fold domains
Family Family family	c.2.1.0 — automated matches

Domain ID domain_id	d3fefa2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.162 — LDH C-terminal domain-like
Superfamily Superfamily superfamily	d.162.1 — LDH C-terminal domain-like
Family Family family	d.162.1.2 — AglA-like glucosidase

Domain ID domain_id	d3fefb1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.2 — NAD(P)-binding Rossmann-fold domains
Superfamily Superfamily superfamily	c.2.1 — NAD(P)-binding Rossmann-fold domains
Family Family family	c.2.1.0 — automated matches

Domain ID domain_id	d3fefb2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.162 — LDH C-terminal domain-like
Superfamily Superfamily superfamily	d.162.1 — LDH C-terminal domain-like
Family Family family	d.162.1.2 — AglA-like glucosidase

Domain ID domain_id	d3fefc1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.2 — NAD(P)-binding Rossmann-fold domains
Superfamily Superfamily superfamily	c.2.1 — NAD(P)-binding Rossmann-fold domains
Family Family family	c.2.1.0 — automated matches

Domain ID domain_id	d3fefc2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.162 — LDH C-terminal domain-like
Superfamily Superfamily superfamily	d.162.1 — LDH C-terminal domain-like
Family Family family	d.162.1.2 — AglA-like glucosidase

Domain ID domain_id	d3fefd1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.2 — NAD(P)-binding Rossmann-fold domains
Superfamily Superfamily superfamily	c.2.1 — NAD(P)-binding Rossmann-fold domains
Family Family family	c.2.1.0 — automated matches

Domain ID domain_id	d3fefd2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.162 — LDH C-terminal domain-like
Superfamily Superfamily superfamily	d.162.1 — LDH C-terminal domain-like
Family Family family	d.162.1.2 — AglA-like glucosidase

CATH v4.4 (4 domains)

Domain ID domain_id	3fefA00
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	1820 — LDH C-terminal domain-like
Homologous superfamily homologous superfamily	10 — AglA-like glucosidase

Domain ID domain_id	3fefB00
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	1820 — LDH C-terminal domain-like
Homologous superfamily homologous superfamily	10 — AglA-like glucosidase

Domain ID domain_id	3fefC00
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	1820 — LDH C-terminal domain-like
Homologous superfamily homologous superfamily	10 — AglA-like glucosidase

Domain ID domain_id	3fefD00
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	1820 — LDH C-terminal domain-like
Homologous superfamily homologous superfamily	10 — AglA-like glucosidase

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Unit-cell length a length_a	81.987 Å
Unit-cell length b length_b	84.843 Å
Unit-cell length c length_c	86.051 Å
Unit-cell angle α angle_alpha	69.80 °
Unit-cell angle β angle_beta	68.10 °
Unit-cell angle γ angle_gamma	64.07 °
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	2.200 Å
Low-resolution limit resolution_low	50.000 Å
R factor r_factor	0.1900
R_work r_work	0.1870
R_free r_free	0.2430

Crystal structure of putative glucosidase lplD from bacillus subtilis

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

Putative glucosidase lplD, ALPHA-GALACTURONIDASE

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

3fef__assembly_2__model_1

3fef__assembly_2__model_1 | I(q)

3fef__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 (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) 12 domains

SCOP 2.08 (8 domains)

CATH v4.4 (4 domains)

7. Citations (1)

Crystal structure of putative glucosidase lplD from bacillus subtilis

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

Putative glucosidase lplD, ALPHA-GALACTURONIDASE

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

3fef__assembly_2__model_1

3fef__assembly_2__model_1 | I(q)

3fef__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 (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) 12 domains

SCOP 2.08 (8 domains)

CATH v4.4 (4 domains)

7. Citations (1)