SAXSdb — 2ixv

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

LYSOZYME

STREPTOCOCCUS PHAGE CP-1

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Monomer	Protein 1 其他Polymer 1	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-N-acetyl-alpha-muramic acid × 1 FORMIC ACID × 1 ALANINE × 1 D-GLUTAMINE × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	LYS_BPCP1
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–339； UniProt 1–339

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	2ixv
Deposition date deposition_date	2006-07-11
Structure title title	Crystal structure of the modular Cpl-1 endolysin complexed with a peptidoglycan analogue (E94Q mutant)
Keywords keywords	;ANTIMICROBIAL, MUEIN HYDROLASE, BACTERIOLYTIC ENZYME, PNEUMOCOCCAL CELL WALL DEGRADATION, LYSOZYME, HYDROLASE, GLYCOSIDASE, MULTIMODULAR ;; 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.

2ixv__assembly_1__model_1

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

Download this curve (.dat)

2ixv__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2ixv__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	24.46 Å
Rg (electron density)	23.37 Å
Total Rg	24.12 Å
Atom count	2814
Residues	338
Excluded volume	49521 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2ixv__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 (6)

Entity 1 Entity 1 polymer

Description description	LYSOZYME
Molecular weight formula_weight	39220.4 kDa
EC 编号 ec_number	3.2.1.17
Mutation mutation	YES
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	3084

MVKKNDLFVDVSSHNGYDITGILEQMGTTNTIIKISESTTYLNPCLSAQVEQSNPIGFYHFARFGGDVAEAEREAQFFLDNVPMQVKYLVLDYQDDPSGDAQANTNACLRFMQMIADAGYKPIYYSYKPFTHDNVDYQQILAQFPNSLWIAGYGLNDGTANFEYFPSMDGIRWWQYSSNPFDKNIVLLDDEEDDKPKTAGTWKQDSKGWWFRRNNGSFPYNKWEKIGGVWYYFDSKGYCLTSEWLKDNEKWYYLKDNGAMATGWVLVGSEWYYMDDSGAMVTGWVKYKNNWYYMTNERGNMVSNEFIKSGKGWYFMNTNGELADNPSFTKEPDGLITVA

Source Source

Source organism organism	STREPTOCOCCUS PHAGE CP-1
Common name common_name	CP-1 BACTERIOPHAGE
NCBI taxonomy ID ncbi_taxonomy_id	10747
Host organism host_organism	ESCHERICHIA COLI DH1

Entity 2 Entity 2 branched

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-N-acetyl-alpha-muramic acid
Molecular weight formula_weight	496.5 kDa
Source method src_method	man
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	FORMIC ACID
Molecular weight formula_weight	46.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	ALANINE
Molecular weight formula_weight	89.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 non-polymer

Description description	D-GLUTAMINE
Molecular weight formula_weight	146.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	270

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6. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d2ixva1
Class class	b — All beta proteins
Fold Fold fold	b.109 — beta-hairpin stack
Superfamily Superfamily superfamily	b.109.1 — Cell wall binding repeat
Family Family family	b.109.1.1 — Cell wall binding repeat

Domain ID domain_id	d2ixva2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.8 — (Trans)glycosidases
Family Family family	c.1.8.8 — 1,4-beta-N-acetylmuraminidase

CATH v4.4 (3 domains)

Domain ID domain_id	2ixvA01
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	80 — Glycosidases

Domain ID domain_id	2ixvA02
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

Domain ID domain_id	2ixvA03
Class class	2 — Mainly Beta
Architecture architecture	20 — Single Sheet
Topology topology	120 — Multimodular pneumococcal cell wall endolysin, domain 3
Homologous superfamily homologous superfamily	10 — Multimodular pneumococcal cell wall endolysin, domain 3

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Unit-cell length a length_a	79.965 Å
Unit-cell length b length_b	96.443 Å
Unit-cell length c length_c	127.073 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	C 2 2 21
Space-group number int_tables_number	20
Crystal system crystal_system	—

Resolution resolution	1.960 Å
Low-resolution limit resolution_low	26.530 Å
R factor r_factor	0.2230
R_work r_work	0.2230
R_free r_free	0.2550

Crystal structure of the modular Cpl-1 endolysin complexed with a peptidoglycan analogue (E94Q mutant)

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

LYSOZYME

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

2ixv__assembly_1__model_1

2ixv__assembly_1__model_1 | I(q)

2ixv__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 (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 branched

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (2 domains)

CATH v4.4 (3 domains)

7. Citations (3)

Crystal structure of the modular Cpl-1 endolysin complexed with a peptidoglycan analogue (E94Q mutant)

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

LYSOZYME

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

2ixv__assembly_1__model_1

2ixv__assembly_1__model_1 | I(q)

2ixv__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 (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 branched

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (2 domains)

CATH v4.4 (3 domains)

7. Citations (3)