SAXSdb — 1zwx

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

sphingomyelinase-c

Listeria ivanovii

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	PHOSPHATE ION × 1 GLYCEROL × 1 water × 1	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 2	PHOSPHATE ION × 2 GLYCEROL × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q9RLV9_LISIV
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–301； UniProt 36–335

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	1zwx
Deposition date deposition_date	2005-06-06
Structure title title	Crystal Structure of SmcL
Keywords keywords	DNase1-like fold, beta-hairpin, 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.

1zwx__assembly_2__model_1

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

Download this curve (.dat)

1zwx__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1zwx__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	27.37 Å
Rg (electron density)	27.10 Å
Total Rg	27.72 Å
Atom count	4624
Residues	576
Excluded volume	81268 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1zwx__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1zwx__assembly_2__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-c
Molecular weight formula_weight	34502.4 kDa
EC 编号 ec_number	3.1.4.12
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	2578

MQASDEYPGNFKITSHNVYLFSRNIYPNWGQMHRADLIAQADYMKNNDVVILNEAFDTSASHRLLNNLREMYPHQTPVIGRSKHGWDKTEGNYSNFALEDGGVAVVSQWPIVEKSQHIFQRGGGADRLSNKGFAYVKIMKNGKPYHIIGTHTQADDSLISKDTSRAIRAEQMQEIQTFIAKKNIPKDEIIFIGGDLNVNYGTDEYHDMLKLLNVSSPANFNGQMATWDPTTNSMLKESYPKAAPEYLDYIFVENGHARPHSWHNKVLHTKSPQWSVKSWFKTYTYQDFSDHYPVVGFTDNN

Source Source

Source organism organism	Listeria ivanovii
NCBI taxonomy ID ncbi_taxonomy_id	1638
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	PHOSPHATE ION
Molecular weight formula_weight	95.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	244

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6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1zwxa1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.151 — DNase I-like
Superfamily Superfamily superfamily	d.151.1 — DNase I-like
Family Family family	d.151.1.3 — Sphingomyelin phosphodiesterase-like

CATH v4.4 (1 domains)

Domain ID domain_id	1zwxA00
Class class	3 — Alpha Beta
Architecture architecture	60 — 4-Layer Sandwich
Topology topology	10 — Deoxyribonuclease I; Chain A
Homologous superfamily homologous superfamily	10 — Endonuclease/exonuclease/phosphatase

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Unit-cell length a length_a	66.860 Å
Unit-cell length b length_b	66.860 Å
Unit-cell length c length_c	180.848 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	6

Space group space_group	P 31 2 1
Space-group number int_tables_number	152
Crystal system crystal_system	—

Resolution resolution	1.900 Å
Low-resolution limit resolution_low	30.670 Å
R factor r_factor	0.2030
R_work r_work	0.2010
R_free r_free	0.2330

Crystal Structure of SmcL

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

sphingomyelinase-c

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

1zwx__assembly_2__model_1

1zwx__assembly_2__model_1 | I(q)

1zwx__assembly_2__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

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) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

7. Citations (1)

Crystal Structure of SmcL

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

sphingomyelinase-c

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

1zwx__assembly_2__model_1

1zwx__assembly_2__model_1 | I(q)

1zwx__assembly_2__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

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) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

7. Citations (1)