SAXSdb — 3a3f

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

Penicillin-binding protein 4

Haemophilus influenzae

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	;(2R,4S)-5,5-dimethyl-2-[(1R)-2-oxo-1-({(2R)-2-[(2-oxoimidazolidin-1-yl)amino]-2-phenylacetyl}amino)ethyl]-1,3-thiazolidine-4-carboxylic acid ; × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A8E0K8_HAEIN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–453； UniProt 28–479 Author chain B； PDBConstruct 2–453； UniProt 28–479

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	3a3f
Deposition date deposition_date	2009-06-12
Structure title title	Crystal structure of penicillin binding protein 4 (dacB) from Haemophilus influenzae,complexed with novel beta-lactam (FMZ)
Keywords keywords	Penicillin Binding Protein 4, PBP4, dacB, 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.

3a3f__assembly_1__model_1

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

Download this curve (.dat)

3a3f__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3a3f__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	30.27 Å
Rg (electron density)	29.43 Å
Total Rg	30.24 Å
Atom count	7066
Residues	906
Excluded volume	126670 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3a3f__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 (3)

Entity 1 Entity 1 polymer

Description description	Penicillin-binding protein 4
Molecular weight formula_weight	49789.9 kDa
EC 编号 ec_number	3.4.16.4
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	7354

MINVSDLTQKLPEGSNAGVIAKNINQNQIIADYNGSTFMLPASTQKVFTAVAAKLALGDQFQFETALLSNGKIQNGNLDGNLIVSFTGDPDLTRGQLYSLLAELKKQGIKKINGDLVLDTSVFSSHDRGLGWIWNDLTMCFNSPPAAANIDNNCFYAELDANKNPGEIVKINVPAQFPIQVFGQVYVADSNEAPYCQLDVVVHDNNRYQVKGCLARQYKPFGLSFAVQNTDAYAAAIIQRQLRKLGIEFNGKVLLPQKPQQGQLLAKHLSKPLPDLLKKMMKKSDNQIADSLFRAVAFNYYKRPASFQLGTLAVKSILQKQGIRFGNSILADGSGLSRHNLVAPKTMLSVLEYIAKNEDKLHLMETFPIAGVDGTISGRGGLISPPLVKNVIAKTGSLKGVYNLAGFMTNARGEKVAFVQFINGYSTGDLESKTKRAPLVQFERNLYNELYKY

Source Source

Source organism organism	Haemophilus influenzae
NCBI taxonomy ID ncbi_taxonomy_id	727
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	;(2R,4S)-5,5-dimethyl-2-[(1R)-2-oxo-1-({(2R)-2-[(2-oxoimidazolidin-1-yl)amino]-2-phenylacetyl}amino)ethyl]-1,3-thiazolidine-4-carboxylic acid ;
Molecular weight formula_weight	435.5 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	288

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6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d3a3fa1
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.3.1.3 — Dac-like

Domain ID domain_id	d3a3fa2
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	d3a3fb1
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.3.1.3 — Dac-like

Domain ID domain_id	d3a3fb2
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 (4 domains)

Domain ID domain_id	3a3fA01
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	3a3fA02
Class class	3 — Alpha Beta
Architecture architecture	50 — 3-Layer(bba) Sandwich
Topology topology	80 — D-tyrosyl-trna(Tyr) Deacylase; Chain: A;
Homologous superfamily homologous superfamily	20 — D-Ala-D-Ala carboxypeptidase C, peptidase S13

Domain ID domain_id	3a3fB01
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	3a3fB02
Class class	3 — Alpha Beta
Architecture architecture	50 — 3-Layer(bba) Sandwich
Topology topology	80 — D-tyrosyl-trna(Tyr) Deacylase; Chain: A;
Homologous superfamily homologous superfamily	20 — D-Ala-D-Ala carboxypeptidase C, peptidase S13

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Unit-cell length a length_a	64.799 Å
Unit-cell length b length_b	92.103 Å
Unit-cell length c length_c	104.454 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	107.95 °
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	2.100 Å
Low-resolution limit resolution_low	19.870 Å
R factor r_factor	0.1921
R_work r_work	0.1897
R_free r_free	0.2356

Crystal structure of penicillin binding protein 4 (dacB) from Haemophilus influenzae,complexed with novel beta-lactam (FMZ)

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

Penicillin-binding protein 4

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

3a3f__assembly_1__model_1

3a3f__assembly_1__model_1 | I(q)

3a3f__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)

Crystal structure of penicillin binding protein 4 (dacB) from Haemophilus influenzae,complexed with novel beta-lactam (FMZ)

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

Penicillin-binding protein 4

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

3a3f__assembly_1__model_1

3a3f__assembly_1__model_1 | I(q)

3a3f__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)