SAXSdb — 5ctv

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

Autolysin

Streptococcus pneumoniae serotype 4

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Heteromer	Protein 3 其他Polymer 1	fragment of peptidoglycan × 2 ;2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-methyl 2-acetamido-3-O-[(1R)-1-carboxyethyl]-2-deoxy-beta-D-glucopyranoside-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-methyl 2-acetamido-3-O-[(1R)-1-carboxyethyl]-2-deoxy-beta-D-glucopyranoside ; × 1 water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	ALYS_STRPN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–182； UniProt 1–180

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	5ctv
Deposition date deposition_date	2015-07-24
Structure title title	Catalytic domain of LytA, the major autolysin of Streptococcus pneumoniae, (C60A, H133A, C136A mutant) complexed with peptidoglycan fragment
Keywords keywords	LytA, pneumococci, autolysis, amidase, peptidoglycan complex, antibiotics, 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.

5ctv__assembly_1__model_1

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

Download this curve (.dat)

5ctv__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5ctv__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	16.13 Å
Rg (electron density)	14.97 Å
Total Rg	16.08 Å
Atom count	1488
Residues	179
Excluded volume	26042 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5ctv__assembly_1__model_1`	trimeric （3）	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	Autolysin
Molecular weight formula_weight	21199.3 kDa
EC 编号 ec_number	3.5.1.28
Mutation mutation	C60A, H133A, C136A
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	1771

ASMEINVSKLRTDLPQVGVQPYRQVHAHSTGNPHSTVQNEADYHWRKDPELGFFSHIVGNGAIMQVGPVDNGAWDVGGGWNAETYAAVELIESHSTKEEFMTDYRLYIELLRNLADEAGLPKTLDTGSLAGIKTAEYATNNQPNNHSDHVDPYPYLAKWGISREQFKHDIENGLTIETGWQKHHHHHH

Source Source

Source organism organism	Streptococcus pneumoniae serotype 4
NCBI taxonomy ID ncbi_taxonomy_id	170187
Host organism host_organism	;Escherichia coli 'BL21-Gold(DE3)pLysS AG' ;

Entity 2 Entity 2 polymer

Description description	fragment of peptidoglycan
Molecular weight formula_weight	489.5 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,E

AEKAA

Entity 3 Entity 3 branched

Description description	;2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-methyl 2-acetamido-3-O-[(1R)-1-carboxyethyl]-2-deoxy-beta-D-glucopyranoside-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-methyl 2-acetamido-3-O-[(1R)-1-carboxyethyl]-2-deoxy-beta-D-glucopyranoside ;
Molecular weight formula_weight	1003.0 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	248

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6. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id	5ctvA00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	80 — Lysozyme-like
Homologous superfamily homologous superfamily	10 — Peptidoglycan recognition protein-like

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Unit-cell length a length_a	44.566 Å
Unit-cell length b length_b	54.623 Å
Unit-cell length c length_c	78.877 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	8

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	1.050 Å
Low-resolution limit resolution_low	44.910 Å
R factor r_factor	0.1348
R_work r_work	0.1338
R_free r_free	0.1527

Catalytic domain of LytA, the major autolysin of Streptococcus pneumoniae, (C60A, H133A, C136A mutant) complexed with peptidoglycan fragment

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

Autolysin

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

5ctv__assembly_1__model_1

5ctv__assembly_1__model_1 | I(q)

5ctv__assembly_1__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 polymer

Polymer Polymer

Entity 3 Entity 3 branched

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

7. Citations (1)

Catalytic domain of LytA, the major autolysin of Streptococcus pneumoniae, (C60A, H133A, C136A mutant) complexed with peptidoglycan fragment

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

Autolysin

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

5ctv__assembly_1__model_1

5ctv__assembly_1__model_1 | I(q)

5ctv__assembly_1__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 polymer

Polymer Polymer

Entity 3 Entity 3 branched

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

7. Citations (1)