SAXSdb — 2f9r

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

Sphingomyelinase D 1

Loxosceles laeta

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	MAGNESIUM ION × 1 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	MAGNESIUM ION × 1 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1 water × 1	Consistent with protein count
3	Protein monomer	Monomer	Protein 1	MAGNESIUM ION × 1 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1 water × 1	Consistent with protein count
4	Protein monomer	Monomer	Protein 1	MAGNESIUM ION × 1 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1 water × 1	Consistent with protein count
5	Protein homooligomer	Homooligomer	Protein 4	MAGNESIUM ION × 4 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 3 water × 4	Consistent with protein count
6	Protein homooligomer	Homooligomer	Protein 2	MAGNESIUM ION × 2 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1 water × 2	Consistent with protein count
7	Protein homooligomer	Homooligomer	Protein 2	MAGNESIUM ION × 2 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SMA1_LOXLA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–285； UniProt 27–311 Author chain B； PDBConstruct 1–285； UniProt 27–311 Author chain C； PDBConstruct 1–285； UniProt 27–311 Author chain D； PDBConstruct 1–285； UniProt 27–311

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	2f9r
Deposition date deposition_date	2005-12-06
Structure title title	Crystal structure of the inactive state of the Smase I, a sphingomyelinase D from Loxosceles laeta venom
Keywords keywords	sphingomyelinase D, catalytic activity, magnesium-binding site, inactive state, 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.

2f9r__assembly_7__model_1

Assembly 7 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

2f9r__assembly_7__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2f9r__assembly_7__model_1 | P(r) · Pending

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

Rg（Guinier）	26.16 Å
Rg (electron density)	24.96 Å
Total Rg	25.80 Å
Atom count	4570
Residues	570
Excluded volume	80955 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2f9r__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2f9r__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`2f9r__assembly_3__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`2f9r__assembly_4__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
5	1	`2f9r__assembly_5__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
6	1	`2f9r__assembly_6__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
7	1	`2f9r__assembly_7__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	Sphingomyelinase D 1
Molecular weight formula_weight	32083.0 kDa
EC 编号 ec_number	3.1.4.41
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	9891

ADNRRPIWNLAHMVNAVAQIPDFLDLGANALEADVTFKGSVPTYTYHGTPCDFGRDCIRWEYFNVFLKTLREYTTPGNAKYRDGFILFVLDLKTGSLSNDQVRPAGENVAKELLQNYWNNGNNGGRAYVVLSLPDIGHYEFVRGFKEVLKKEGHEDLLEKVGYDFSGPYLPSLPTLDATHEAYKKAGVDGHIWLSDGLTNFSPLGDMARLKEAIKSRDSANGFINKIYYWSVDKVSTTKAALDVGVDGIMTNYPNVLIGVLKESGYNDKYRLATYDDNPWETFKN

Source Source

Source organism organism	Loxosceles laeta
NCBI taxonomy ID ncbi_taxonomy_id	58217
Host organism host_organism	Escherichia coli BL21

Entity 2 Entity 2 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 non-polymer

Description description	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
Molecular weight formula_weight	238.3 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	507

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6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id	2f9rA00
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	190 — Phosphatidylinositol (PI) phosphodiesterase

Domain ID domain_id	2f9rB00
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	190 — Phosphatidylinositol (PI) phosphodiesterase

Domain ID domain_id	2f9rC00
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	190 — Phosphatidylinositol (PI) phosphodiesterase

Domain ID domain_id	2f9rD00
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	190 — Phosphatidylinositol (PI) phosphodiesterase

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Unit-cell length a length_a	140.587 Å
Unit-cell length b length_b	140.587 Å
Unit-cell length c length_c	113.608 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	24

Space group space_group	P 65
Space-group number int_tables_number	170
Crystal system crystal_system	—

Resolution resolution	1.850 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.1896
R_work r_work	0.1873
R_free r_free	0.2340

Crystal structure of the inactive state of the Smase I, a sphingomyelinase D from Loxosceles laeta venom

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

Sphingomyelinase D 1

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

2f9r__assembly_7__model_1

2f9r__assembly_7__model_1 | I(q)

2f9r__assembly_7__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) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)

Crystal structure of the inactive state of the Smase I, a sphingomyelinase D from Loxosceles laeta venom

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

Sphingomyelinase D 1

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

2f9r__assembly_7__model_1

2f9r__assembly_7__model_1 | I(q)

2f9r__assembly_7__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) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)