SAXSdb — 4u3t

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

Penicillin-binding protein 2

Neisseria gonorrhoeae FA6140

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PBP2_NEIGO
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 6–330； UniProt 237–574 Author chain B； PDBConstruct 6–330； UniProt 237–574

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	4u3t
Deposition date deposition_date	2014-07-22
Structure title title	Crystal structure of the transpeptidase domain of Neisseria gonorrhoeae penicillin-binding protein 2 derived from the penicillin-resistant strain 6140
Keywords keywords	penicillin-binding protein, transpeptidase domain, peptidoglycan synthesis, antibiotic resistance, 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.

4u3t__assembly_2__model_1

Assembly 2 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

4u3t__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4u3t__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	19.70 Å
Rg (electron density)	18.46 Å
Total Rg	19.39 Å
Atom count	2376
Residues	314
Excluded volume	42389 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4u3t__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`4u3t__assembly_2__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 (2)

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6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d4u3ta1
Class class	e — Multi-domain proteins (alpha and beta)
Fold Fold fold	e.3 — beta-lactamase/transpeptidase-like
Superfamily Superfamily superfamily	e.3.1 — beta-lactamase/transpeptidase-like
Family Family family	e.3.1.0 — automated matches

Domain ID domain_id	d4u3ta2
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	d4u3tb1
Class class	e — Multi-domain proteins (alpha and beta)
Fold Fold fold	e.3 — beta-lactamase/transpeptidase-like
Superfamily Superfamily superfamily	e.3.1 — beta-lactamase/transpeptidase-like
Family Family family	e.3.1.0 — automated matches

Domain ID domain_id	d4u3tb2
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	4u3tA00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	710 — Beta-lactamase
Homologous superfamily homologous superfamily	10 — DD-peptidase/beta-lactamase superfamily

Domain ID domain_id	4u3tB00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	710 — Beta-lactamase
Homologous superfamily homologous superfamily	10 — DD-peptidase/beta-lactamase superfamily

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Unit-cell length a length_a	44.500 Å
Unit-cell length b length_b	77.400 Å
Unit-cell length c length_c	88.000 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	92.50 °
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	2.200 Å
Low-resolution limit resolution_low	35.450 Å
R factor r_factor	0.1953
R_work r_work	0.1927
R_free r_free	0.2432

Description description	Penicillin-binding protein 2
Molecular weight formula_weight	35411.3 kDa
EC 编号 ec_number	3.4.16.4
Mutation mutation	D346a, F504L, A510V, A516G, P551S
Source method src_method	man
Copy count entity_count	2

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	4911

Crystal structure of the transpeptidase domain of Neisseria gonorrhoeae penicillin-binding protein 2 derived from the penicillin-resistant strain 6140

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

Penicillin-binding protein 2

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

4u3t__assembly_2__model_1

4u3t__assembly_2__model_1 | I(q)

4u3t__assembly_2__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 water

6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (4 domains)

CATH v4.4 (2 domains)

7. Citations (1)

Source organism organism	Neisseria gonorrhoeae FA6140
NCBI taxonomy ID ncbi_taxonomy_id	528353
Host organism host_organism	Escherichia coli

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	92

Crystal structure of the transpeptidase domain of Neisseria gonorrhoeae penicillin-binding protein 2 derived from the penicillin-resistant strain 6140

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

Penicillin-binding protein 2

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

4u3t__assembly_2__model_1

4u3t__assembly_2__model_1 | I(q)

4u3t__assembly_2__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 water

6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (4 domains)

CATH v4.4 (2 domains)

7. Citations (1)