SAXSdb — 4x36

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

Autolysin

Streptococcus pneumoniae TIGR4

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	GLYCEROL × 12 ZINC ION × 2 CHOLINE ION × 10 water × 2	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 1–318； UniProt 1–318

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	4x36
Deposition date deposition_date	2014-11-28
Structure title title	Crystal structure of the autolysin LytA from Streptococcus pneumoniae TIGR4
Keywords keywords	Autolysin, amidase, 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.

4x36__assembly_1__model_1

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

Download this curve (.dat)

4x36__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4x36__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	49.85 Å
Rg (electron density)	49.75 Å
Total Rg	49.84 Å
Atom count	5320
Residues	622
Excluded volume	93872 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4x36__assembly_1__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 (5)

Entity 1 Entity 1 polymer

Description description	Autolysin
Molecular weight formula_weight	36914.5 kDa
EC 编号 ec_number	3.5.1.28
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	2909

MEINVSKLRTDLPQVGVQPYRQVHAHSTGNPHSTVQNEADYHWRKDPELGFFSHIVGNGCIMQVGPVDNGAWDVGGGWNAETYAAVELIESHSTKEEFMTDYRLYIELLRNLADEAGLPKTLDTGSLAGIKTHEYCTNNQPNNHSDHVDPYPYLAKWGISREQFKHDIENGLTIETGWQKNDTGYWYVHSDGSYPKDKFEKINGTWYYFDSSGYMLADRWRKHTDGNWYWFDNSGEMATGWKKIADKWYYFNEEGAMKTGWVKYKDTWYYLDAKEGAMVSNAFIQSADGTGWYYLKPDGTLADKPEFTVEPDGLITVK

Source Source

Source organism organism	Streptococcus pneumoniae TIGR4
NCBI taxonomy ID ncbi_taxonomy_id	170187
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 3 Entity 3 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	CHOLINE ION
Molecular weight formula_weight	104.2 kDa
Source method src_method	syn
Copy count entity_count	5

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	241

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6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	4x36A01
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

Domain ID domain_id	4x36A02
Class class	2 — Mainly Beta
Architecture architecture	10 — Ribbon
Topology topology	270 — left handed beta-beta-3-solenoid
Homologous superfamily homologous superfamily	10 — Cholin Binding

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Unit-cell length a length_a	101.282 Å
Unit-cell length b length_b	101.282 Å
Unit-cell length c length_c	119.577 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 43 21 2
Space-group number int_tables_number	96
Crystal system crystal_system	—

Resolution resolution	2.101 Å
Low-resolution limit resolution_low	46.632 Å
R factor r_factor	0.1836
R_work r_work	0.1828
R_free r_free	0.1990

Crystal structure of the autolysin LytA from Streptococcus pneumoniae TIGR4

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

4x36__assembly_1__model_1

4x36__assembly_1__model_1 | I(q)

4x36__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 (5)

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 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)

Crystal structure of the autolysin LytA from Streptococcus pneumoniae TIGR4

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

4x36__assembly_1__model_1

4x36__assembly_1__model_1 | I(q)

4x36__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 (5)

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 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)