1xp4

Crystal structure of a peptidoglycan synthesis regulatory factor (PBP3) from Streptococcus pneumoniae

Method: X-RAY DIFFRACTION

▼

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

D-alanyl-D-alanine carboxypeptidase

Streptococcus pneumoniae R6

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	SULFATE ION × 1 IODIDE ION × 4 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	SULFATE ION × 1 IODIDE ION × 4 water × 1	Consistent with protein count
3	Protein monomer	Monomer	Protein 1	SULFATE ION × 1 IODIDE ION × 4 water × 1	Consistent with protein count
4	Protein monomer	Monomer	Protein 1	SULFATE ION × 1 IODIDE ION × 4 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q8DQ99_STRR6
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–379； UniProt 16–394 Author chain B； PDBConstruct 1–379； UniProt 16–394 Author chain C； PDBConstruct 1–379； UniProt 16–394 Author chain D； PDBConstruct 1–379； UniProt 16–394

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	1xp4
Deposition date deposition_date	2004-10-08
Structure title title	Crystal structure of a peptidoglycan synthesis regulatory factor (PBP3) from Streptococcus pneumoniae
Keywords keywords	five-stranded antiparallel beta-sheet, omega-like loop, HYDROLASE; HYDROLASE
Experimental Method method	X-RAY DIFFRACTION

▼

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.

1xp4__assembly_3__model_1

Assembly 3 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

1xp4__assembly_3__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1xp4__assembly_3__model_1 | P(r) · Pending

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

Rg（Guinier）	23.50 Å
Rg (electron density)	22.79 Å
Total Rg	23.26 Å
Atom count	2759
Residues	350
Excluded volume	49331 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1xp4__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1xp4__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`1xp4__assembly_3__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`1xp4__assembly_4__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	D-alanyl-D-alanine carboxypeptidase
Molecular weight formula_weight	41566.1 kDa
EC 编号 ec_number	3.4.16.4
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	11150

GVSTAVAQDFTIAAKHAIAVEANTGKILYEKDATQPVEIASITKLITVYLVYEALENGSITLSTPVDISDYPYQLTTNSEASNIPMEARNYTVEELLEATLVSSANSAAIALAEKIAGSEKDFVDMMRAKLLEWGIQDATVVNTTGLNNETLGDNIYPGSKKDEENKLSAYDVAIVARNLIKKYPQVLEITKKPSSTFAGMTITSTNYMLEGMPAYRGGFDGLKTGTTDKAGESFVGTTVEKGMRVITVVLNADHQDNNPYARFTATSSLMDYISSTFTLRKIVQQGDAYQDSKAPVQDGKEDTVIAVAPEDIYLIERVGNQSSQSVQFTPDSKAIPAPLEAGTVVGHLTYEDKDLIGQGYITTERPSFEMVADKKIEK

Source Source

Source organism organism	Streptococcus pneumoniae R6
NCBI taxonomy ID ncbi_taxonomy_id	171101
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 non-polymer

Description description	IODIDE ION
Molecular weight formula_weight	126.9 kDa
Source method src_method	syn
Copy count entity_count	16

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	461

▼

6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

Domain ID domain_id	d1xp4a1
Class class	b — All beta proteins
Fold Fold fold	b.105 — Penicillin-binding protein associated domain
Superfamily Superfamily superfamily	b.105.1 — Penicillin-binding protein associated domain
Family Family family	b.105.1.1 — PBP5 C-terminal domain-like

Domain ID domain_id	d1xp4a2
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.3.1.1 — beta-Lactamase/D-ala carboxypeptidase

Domain ID domain_id	d1xp4b1
Class class	b — All beta proteins
Fold Fold fold	b.105 — Penicillin-binding protein associated domain
Superfamily Superfamily superfamily	b.105.1 — Penicillin-binding protein associated domain
Family Family family	b.105.1.1 — PBP5 C-terminal domain-like

Domain ID domain_id	d1xp4b2
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.3.1.1 — beta-Lactamase/D-ala carboxypeptidase

Domain ID domain_id	d1xp4c1
Class class	b — All beta proteins
Fold Fold fold	b.105 — Penicillin-binding protein associated domain
Superfamily Superfamily superfamily	b.105.1 — Penicillin-binding protein associated domain
Family Family family	b.105.1.1 — PBP5 C-terminal domain-like

Domain ID domain_id	d1xp4c2
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.3.1.1 — beta-Lactamase/D-ala carboxypeptidase

Domain ID domain_id	d1xp4d1
Class class	b — All beta proteins
Fold Fold fold	b.105 — Penicillin-binding protein associated domain
Superfamily Superfamily superfamily	b.105.1 — Penicillin-binding protein associated domain
Family Family family	b.105.1.1 — PBP5 C-terminal domain-like

Domain ID domain_id	d1xp4d2
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.3.1.1 — beta-Lactamase/D-ala carboxypeptidase

CATH v4.4 (8 domains)

Domain ID domain_id	1xp4A01
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	1xp4A02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	410 — Peptidoglycan synthesis regulatory factor (PBP3), Domain 2
Homologous superfamily homologous superfamily	10 — D-Ala-D-Ala carboxypeptidase, C-terminal domain

Domain ID domain_id	1xp4B01
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	1xp4B02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	410 — Peptidoglycan synthesis regulatory factor (PBP3), Domain 2
Homologous superfamily homologous superfamily	10 — D-Ala-D-Ala carboxypeptidase, C-terminal domain

Domain ID domain_id	1xp4C01
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	1xp4C02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	410 — Peptidoglycan synthesis regulatory factor (PBP3), Domain 2
Homologous superfamily homologous superfamily	10 — D-Ala-D-Ala carboxypeptidase, C-terminal domain

Domain ID domain_id	1xp4D01
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	1xp4D02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	410 — Peptidoglycan synthesis regulatory factor (PBP3), Domain 2
Homologous superfamily homologous superfamily	10 — D-Ala-D-Ala carboxypeptidase, C-terminal domain

▶

Unit-cell length a length_a	87.608 Å
Unit-cell length b length_b	120.839 Å
Unit-cell length c length_c	177.076 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	16

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	65.840 Å
R factor r_factor	0.2370
R_work r_work	0.2370
R_free r_free	0.2780

Crystal structure of a peptidoglycan synthesis regulatory factor (PBP3) from Streptococcus pneumoniae

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

D-alanyl-D-alanine carboxypeptidase

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

1xp4__assembly_3__model_1

1xp4__assembly_3__model_1 | I(q)

1xp4__assembly_3__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 (4)

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 water

6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

CATH v4.4 (8 domains)

7. Citations (1)

Crystal structure of a peptidoglycan synthesis regulatory factor (PBP3) from Streptococcus pneumoniae

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

D-alanyl-D-alanine carboxypeptidase

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

1xp4__assembly_3__model_1

1xp4__assembly_3__model_1 | I(q)

1xp4__assembly_3__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 (4)

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 water

6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

CATH v4.4 (8 domains)

7. Citations (1)