1xov

The crystal structure of the listeria monocytogenes bacteriophage PSA endolysin PlyPSA

Method: X-RAY DIFFRACTION

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

Ply protein

Listeria phage PSA

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	ZINC ION × 1 SULFATE ION × 1 CHLORIDE ION × 1 GLUTAMIC ACID × 1 LYSINE × 1 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q8W5Y8_9CAUD
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 13–326； UniProt 1–314

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	1xov
Deposition date deposition_date	2004-10-07
Structure title title	The crystal structure of the listeria monocytogenes bacteriophage PSA endolysin PlyPSA
Keywords keywords	alpha/beta hydrolase, multi-domain, 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.

1xov__assembly_1__model_1

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

Download this curve (.dat)

1xov__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1xov__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	26.76 Å
Rg (electron density)	26.80 Å
Total Rg	27.46 Å
Atom count	2521
Residues	315
Excluded volume	45063 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1xov__assembly_1__model_1`	monomeric （1）	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 (8)

Entity 1 Entity 1 polymer

Description description	Ply protein
Molecular weight formula_weight	36645.9 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	2828

ASWSHPQFEKGAMSNYSMSRGHSDKCVGAEDILSEIKEAEKVLNAASDELKREGHNVKTFIDRTSTTQSANLNKIVNWHNANPADVHISVHLNAGKGTGVEVWYYAGDEKGRKLAVEISAKMAKALGLPNRGAKATKDLRFLNSTKGTAVLLEVCFVDRKEDANAIHKSGMYDKLGIAIAEGLTGKTVAAKNPNRHSGAVVDSVPMLSKMDFKSSPIKMYKAGSSLLVYEHNKYWYKAYINDKLCYIYKSFCISNGKKDAKGRIKVRIKSAKDLRIPVWNNTKLNSGKIKWYSPGTKLSWYDNKKGYLELWYEKDGWYYTANYFLK

Source Source

Source organism organism	Listeria phage PSA
NCBI taxonomy ID ncbi_taxonomy_id	171618
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

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

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	1

Entity 4 Entity 4 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 non-polymer

Description description	GLUTAMIC ACID
Molecular weight formula_weight	147.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 non-polymer

Description description	LYSINE
Molecular weight formula_weight	147.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 7 Entity 7 non-polymer

Description description	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
Molecular weight formula_weight	122.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 8 Entity 8 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	307

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6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d1xova1
Class class	b — All beta proteins
Fold Fold fold	b.34 — SH3-like barrel
Superfamily Superfamily superfamily	b.34.11 — Prokaryotic SH3-related domain
Family Family family	b.34.11.4 — Ply C-terminal domain-like

Domain ID domain_id	d1xova2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.56 — Phosphorylase/hydrolase-like
Superfamily Superfamily superfamily	c.56.5 — Zn-dependent exopeptidases
Family Family family	c.56.5.6 — N-acetylmuramoyl-L-alanine amidase-like

Domain ID domain_id	d1xova3
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

CATH v4.4 (3 domains)

Domain ID domain_id	1xovA01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	630 — Aminopeptidase
Homologous superfamily homologous superfamily	40 — Zn-dependent exopeptidases

Domain ID domain_id	1xovA02
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	30 — SH3 type barrels.
Homologous superfamily homologous superfamily	40 — SH3 Domains

Domain ID domain_id	1xovA03
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	30 — SH3 type barrels.
Homologous superfamily homologous superfamily	40 — SH3 Domains

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Unit-cell length a length_a	90.586 Å
Unit-cell length b length_b	90.586 Å
Unit-cell length c length_c	213.667 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	12

Space group space_group	P 61 2 2
Space-group number int_tables_number	178
Crystal system crystal_system	—

Resolution resolution	1.800 Å
Low-resolution limit resolution_low	25.000 Å
R factor r_factor	0.1716
R_work r_work	0.1702
R_free r_free	0.1983

The crystal structure of the listeria monocytogenes bacteriophage PSA endolysin PlyPSA

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

Ply protein

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

1xov__assembly_1__model_1

1xov__assembly_1__model_1 | I(q)

1xov__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 (8)

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 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 water

6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

CATH v4.4 (3 domains)

7. Citations (1)

The crystal structure of the listeria monocytogenes bacteriophage PSA endolysin PlyPSA

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

Ply protein

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

1xov__assembly_1__model_1

1xov__assembly_1__model_1 | I(q)

1xov__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 (8)

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 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 water

6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

CATH v4.4 (3 domains)

7. Citations (1)