SAXSdb — 3dnm

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

Esterase/lipase

uncultured bacterium

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	BETA-MERCAPTOETHANOL × 1 SULFATE ION × 2 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	BETA-MERCAPTOETHANOL × 1 SULFATE ION × 7 water × 1	Consistent with protein count
3	Protein monomer	Monomer	Protein 1	BETA-MERCAPTOETHANOL × 1 SULFATE ION × 2 water × 1	Consistent with protein count
4	Protein monomer	Monomer	Protein 1	BETA-MERCAPTOETHANOL × 1 SULFATE ION × 3 water × 1	Consistent with protein count
5	Protein homooligomer	Homooligomer	Protein 4	BETA-MERCAPTOETHANOL × 4 SULFATE ION × 10 water × 4	Consistent with protein count
6	Protein homooligomer	Homooligomer	Protein 4	BETA-MERCAPTOETHANOL × 4 SULFATE ION × 18 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q0GMU1_9BACT
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 15–323； UniProt 1–309 Author chain B； PDBConstruct 15–323； UniProt 1–309 Author chain C； PDBConstruct 15–323； UniProt 1–309 Author chain D； PDBConstruct 15–323； UniProt 1–309

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	3dnm
Deposition date deposition_date	2008-07-02
Structure title title	Crystal Structure Hormone-Sensitive Lipase from a Metagenome Library
Keywords keywords	alpha/beta hydrolase fold, 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.

3dnm__assembly_3__model_1

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

Download this curve (.dat)

3dnm__assembly_3__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3dnm__assembly_3__model_1 | P(r) · Pending

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

Rg（Guinier）	18.80 Å
Rg (electron density)	17.48 Å
Total Rg	18.48 Å
Atom count	2201
Residues	291
Excluded volume	39229 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3dnm__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3dnm__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`3dnm__assembly_3__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`3dnm__assembly_4__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
5	1	`3dnm__assembly_5__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
6	1	`3dnm__assembly_6__model_1`	tetrameric （4）	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	Esterase/lipase
Molecular weight formula_weight	36006.9 kDa
EC 编号 ec_number	3.1.1.-
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	9129

MASMTGGNNMGRGSMGAMDQEIGTVTDTKMDPRDFLQLLKINAEKAEKNLPLDQKRAGMEALCERFPRAEGVELTLTDLGGVPCIRQATDGAGAAHILYFHGGGYISGSPSTHLVLTTQLAKQSSATLWSLDYRLAPENPFPAAVDDCVAAYRALLKTAGSADRIIIAGDSAGGGLTTASMLKAKEDGLPMPAGLVMLSPFVDLTLSRWSNSNLADRDFLAEPDTLGEMSELYVGGEDRKNPLISPVYADLSGLPEMLIHVGSEEALLSDSTTLAERAGAAGVSVELKIWPDMPHVFQMYGKFVNAADISIKEICHWISARISKLAAALEHHHHHH

Source Source

Source organism organism	uncultured bacterium
NCBI taxonomy ID ncbi_taxonomy_id	77133
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	BETA-MERCAPTOETHANOL
Molecular weight formula_weight	78.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	14

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	204

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6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d3dnma_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.69 — alpha/beta-Hydrolases
Superfamily Superfamily superfamily	c.69.1 — alpha/beta-Hydrolases
Family Family family	c.69.1.0 — automated matches

Domain ID domain_id	d3dnmb_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.69 — alpha/beta-Hydrolases
Superfamily Superfamily superfamily	c.69.1 — alpha/beta-Hydrolases
Family Family family	c.69.1.0 — automated matches

Domain ID domain_id	d3dnmc_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.69 — alpha/beta-Hydrolases
Superfamily Superfamily superfamily	c.69.1 — alpha/beta-Hydrolases
Family Family family	c.69.1.0 — automated matches

Domain ID domain_id	d3dnmd_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.69 — alpha/beta-Hydrolases
Superfamily Superfamily superfamily	c.69.1 — alpha/beta-Hydrolases
Family Family family	c.69.1.0 — automated matches

CATH v4.4 (4 domains)

Domain ID domain_id	3dnmA00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1820 — Alpha/Beta hydrolase fold, catalytic domain

Domain ID domain_id	3dnmB00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1820 — Alpha/Beta hydrolase fold, catalytic domain

Domain ID domain_id	3dnmC00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1820 — Alpha/Beta hydrolase fold, catalytic domain

Domain ID domain_id	3dnmD00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1820 — Alpha/Beta hydrolase fold, catalytic domain

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Unit-cell length a length_a	117.321 Å
Unit-cell length b length_b	126.828 Å
Unit-cell length c length_c	233.393 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	32

Space group space_group	I 21 21 21
Space-group number int_tables_number	24
Crystal system crystal_system	—

Resolution resolution	2.800 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.2330
R_work r_work	0.2330
R_free r_free	0.2820

Crystal Structure Hormone-Sensitive Lipase from a Metagenome Library

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

Esterase/lipase

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

3dnm__assembly_3__model_1

3dnm__assembly_3__model_1 | I(q)

3dnm__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

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)

Crystal Structure Hormone-Sensitive Lipase from a Metagenome Library

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

Esterase/lipase

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

3dnm__assembly_3__model_1

3dnm__assembly_3__model_1 | I(q)

3dnm__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

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)