SAXSdb — 4ekp

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

Lysozyme

Enterobacteria phage T4

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	BETA-MERCAPTOETHANOL × 2 NITROBENZENE × 1 SULFATE ION × 3 ACETATE ION × 2 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	BETA-MERCAPTOETHANOL × 2 NITROBENZENE × 1 SULFATE ION × 2 ACETATE ION × 1 2-HYDROXYETHYL DISULFIDE × 1 water × 1	Consistent with protein count
3	Protein homooligomer	Homooligomer	Protein 2	BETA-MERCAPTOETHANOL × 4 NITROBENZENE × 2 SULFATE ION × 5 ACETATE ION × 3 2-HYDROXYETHYL DISULFIDE × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	LYS_BPT4
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 24–187； UniProt 1–164 Author chain B； PDBConstruct 24–187； UniProt 1–164

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	4ekp
Deposition date deposition_date	2012-04-09
Structure title title	T4 Lysozyme L99A/M102H with Nitrobenzene Bound
Keywords keywords	hydrolase, alkylation of Cys97; 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.

4ekp__assembly_1__model_1

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

Download this curve (.dat)

4ekp__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4ekp__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	17.92 Å
Rg (electron density)	16.84 Å
Total Rg	17.87 Å
Atom count	1409
Residues	175
Excluded volume	24971 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4ekp__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`4ekp__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`4ekp__assembly_3__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 (7)

Entity 1 Entity 1 polymer

Description description	Lysozyme
Molecular weight formula_weight	21404.4 kDa
EC 编号 ec_number	3.2.1.17
Mutation mutation	T21C/S38D/L99A/M102H/E108V/S117V/T142C/N144D
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	3292

MGHHHHHHDYDIPTTENLYFQGSMNIFEMLRIDEGLRLKIYKDCEGYYTIGIGHLLTKSPDLNAAKSELDKAIGRNCNGVITKDEAEKLFNQDVDAAVRGILRNAKLKPVYDSLDAVRRCAAINHVFQMGVTGVAGFTNVLRMLQQKRWDEAAVNLAKSRWYNQCPDRAKRVITTFRTGTWDAYKNL

Source Source

Source organism organism	Enterobacteria phage T4
NCBI taxonomy ID ncbi_taxonomy_id	10665
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	BETA-MERCAPTOETHANOL
Molecular weight formula_weight	78.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 non-polymer

Description description	NITROBENZENE
Molecular weight formula_weight	123.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	5

Entity 5 Entity 5 non-polymer

Description description	ACETATE ION
Molecular weight formula_weight	59.0 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 6 Entity 6 non-polymer

Description description	2-HYDROXYETHYL DISULFIDE
Molecular weight formula_weight	154.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 7 Entity 7 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	336

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6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d4ekpa1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.2 — Lysozyme-like
Superfamily Superfamily superfamily	d.2.1 — Lysozyme-like
Family Family family	d.2.1.3 — Phage lysozyme

Domain ID domain_id	d4ekpa2
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

Domain ID domain_id	d4ekpb1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.2 — Lysozyme-like
Superfamily Superfamily superfamily	d.2.1 — Lysozyme-like
Family Family family	d.2.1.3 — Phage lysozyme

Domain ID domain_id	d4ekpb2
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 (2 domains)

Domain ID domain_id	4ekpA00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	530 — Lysozyme
Homologous superfamily homologous superfamily	40 —

Domain ID domain_id	4ekpB00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	530 — Lysozyme
Homologous superfamily homologous superfamily	40 —

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Unit-cell length a length_a	48.370 Å
Unit-cell length b length_b	75.530 Å
Unit-cell length c length_c	52.720 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	93.22 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	1.640 Å
Low-resolution limit resolution_low	43.185 Å
R factor r_factor	0.1705
R_work r_work	0.1694
R_free r_free	0.1963

T4 Lysozyme L99A/M102H with Nitrobenzene Bound

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

4ekp__assembly_1__model_1

4ekp__assembly_1__model_1 | I(q)

4ekp__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 (7)

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 water

6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (4 domains)

CATH v4.4 (2 domains)

7. Citations (1)

T4 Lysozyme L99A/M102H with Nitrobenzene Bound

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

4ekp__assembly_1__model_1

4ekp__assembly_1__model_1 | I(q)

4ekp__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 (7)

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 water

6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (4 domains)

CATH v4.4 (2 domains)

7. Citations (1)