SAXSdb — 2j9p

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

D-alanyl-D-alanine carboxypeptidase DacC

Bacillus subtilis

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	(2R)-2-AMINO-7-{[(1R)-1-CARBOXYETHYL]AMINO}-7-OXOHEPTANOIC ACID × 1 D-ALANINE × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	(2R)-2-AMINO-7-{[(1R)-1-CARBOXYETHYL]AMINO}-7-OXOHEPTANOIC ACID × 1 D-ALANINE × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	DACC_BACSU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–462； UniProt 30–491 Author chain B； PDBConstruct 1–462； UniProt 30–491

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	2j9p
Deposition date deposition_date	2006-11-15
Structure title title	Crystal structure of the Bacillus subtilis PBP4a, and its complex with a peptidoglycan mimetic peptide.
Keywords keywords	;D-ALA-D-ALA- CARBOXYPEPTIDASE, PEPTIDOGLYCAN SYNTHESIS, PENICILLIN-BINDING PROTEIN, PEPTIDOGLYCAN, CELL DIVISION, BACILLUS SUBTILIS, CELL WALL, HYDROLASE, CELL SHAPE, CELL CYCLE ;; 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.

2j9p__assembly_2__model_1

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

Download this curve (.dat)

2j9p__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2j9p__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	24.67 Å
Rg (electron density)	23.88 Å
Total Rg	24.76 Å
Atom count	3483
Residues	458
Excluded volume	61983 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2j9p__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2j9p__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 (3)

Entity 1 Entity 1 polymer

Description description	D-alanyl-D-alanine carboxypeptidase DacC
Molecular weight formula_weight	49762.9 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	6966

AEKQDALSGQIDKILADHPALEGAMAGITVRSAETGAVLYEHSGDTRMRPASSLKLLTAAAALSVLGENYSFTTEVRTDGTLKGKKLNGNLYLKGKGDPTLLPSDFDKMAEILKHSGVKVIKGNLIGDDTWHDDMRLSPDMPWSDEYTYYGAPISALTASPNEDYDAGTVIVEVTPNQKEGEEPAVSVSPKTDYITIKNDAKTTAAGSEKDLTIEREHGTNTITIEGSVPVDANKTKEWISVWEPAGYALDLFKQSLKKQGITVKGDIKTGEAPSSSDVLLSHRSMPLSKLFVPFMKLSNNGHAEVLVKEMGKVKKGEGSWEKGLEVLNSTLPEFGVDSKSLVLRDGSGISHIDAVSSDQLSQLLYDIQDQSWFSAYLNSLPVAGNPDRMVGGTLRNRMKGTPAQGKVRAKTGSLSTVSSLSGYAETKSGKKLVFSILLNGLIDEEDGKDIEDQIAVILANQ

Source Source

Source organism organism	Bacillus subtilis
NCBI taxonomy ID ncbi_taxonomy_id	224308
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	(2R)-2-AMINO-7-{[(1R)-1-CARBOXYETHYL]AMINO}-7-OXOHEPTANOIC ACID
Molecular weight formula_weight	246.3 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	D-ALANINE
Molecular weight formula_weight	89.1 kDa
Source method src_method	syn
Copy count entity_count	2

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6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d2j9pa1
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	d2j9pb1
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

CATH v4.4 (4 domains)

Domain ID domain_id	2j9pA01
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	2j9pA02
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	2j9pB01
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	2j9pB02
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	73.859 Å
Unit-cell length b length_b	77.586 Å
Unit-cell length c length_c	164.739 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	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.800 Å
Low-resolution limit resolution_low	19.900 Å
R factor r_factor	0.2080
R_work r_work	0.2080
R_free r_free	0.2900

Crystal structure of the Bacillus subtilis PBP4a, and its complex with a peptidoglycan mimetic peptide.

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

D-alanyl-D-alanine carboxypeptidase DacC

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

2j9p__assembly_2__model_1

2j9p__assembly_2__model_1 | I(q)

2j9p__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

CATH v4.4 (4 domains)

7. Citations (1)

Crystal structure of the Bacillus subtilis PBP4a, and its complex with a peptidoglycan mimetic peptide.

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

D-alanyl-D-alanine carboxypeptidase DacC

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

2j9p__assembly_2__model_1

2j9p__assembly_2__model_1 | I(q)

2j9p__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

CATH v4.4 (4 domains)

7. Citations (1)