SAXSdb — 2olv

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

Penicillin-binding protein 2

Staphylococcus aureus

State in the Current Structure

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

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q2YY56_STAAB
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–669； UniProt 60–727 Author chain B； PDBConstruct 2–669； UniProt 60–727

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	2olv
Deposition date deposition_date	2007-01-19
Structure title title	Structural Insight Into the Transglycosylation Step Of Bacterial Cell Wall Biosynthesis : Donor Ligand Complex
Keywords keywords	transpeptidase fold, glycosyltransferase family 51, lysozyme fold, TRANSFERASE; TRANSFERASE
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.

2olv__assembly_1__model_1

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

Download this curve (.dat)

2olv__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2olv__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	32.94 Å
Rg (electron density)	33.17 Å
Total Rg	33.39 Å
Atom count	4935
Residues	605
Excluded volume	86725 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2olv__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2olv__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)

Entity 1 Entity 1 polymer

Description description	Penicillin-binding protein 2
Molecular weight formula_weight	74640.1 kDa
EC 编号 ec_number	2.3.2.-
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	9878

MKAPAFTEAKLQDPIPAKIYDKNGELVKTLDNGQRHEHVNLKDVPKSMKDAVLATEDNRFYEHGALDYKRLFGAIGKNLTGGFGSEGASTLTQQVVKDAFLSQHKSIGRKAQEAYLSYRLEQEYSKDDIFQVYLNKIYYSDGVTGIKAAAKYYFNKDLKDLNLAEEAYLAGLPQVPNNYNIYDHPKAAEDRKNTVLYLMHYHKRITDKQWEDAKKIDLKANLVNRTPEERQNIDTNQDSEYNSYVNFVKSELMNNKAFKDENLGNVLQSGIKIYTNMDKDVQKTLQNDVDNGSFYKNKDQQVGATILDSKTGGLVAISGGRDFKDVVNRNQATDPHPTGSSLKPFLAYGPAIENMKWATNHAIQDESSYQVDGSTFRNYDTKSHGTVSIYDALRQSFNIPALKAWQSVKQNAGNDAPKKFAAKLGLNYEGDIGPSEVLGGSASEFSPTQLASAFAAIANGGTYNNAHSIQKVVTRDGETIEYDHTSHKAMSDYTAYMLAEMLKGTFKPYGSAYGHGVSGVNMGAKTGTGTYGAETYSQYNLPDNAAKDVWINGFTPQYTMSVWMGFSKVKQYGENSFVGHSQQEYPQFLYENVMSKISSRDGEDFKRPSSVSGSIPSINVSGSQDNNTTNRSTHGGSDTSANSSGTAQSNNNTRSQQSRNSGGLTGIFN

Source Source

Source organism organism	Staphylococcus aureus
NCBI taxonomy ID ncbi_taxonomy_id	1280
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	MOENOMYCIN
Molecular weight formula_weight	1580.6 kDa
Source method src_method	syn
Copy count entity_count	2

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6. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d2olva1
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.2.1.10 — PBP transglycosylase domain-like

Domain ID domain_id	d2olva2
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	d2olvb1
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.2.1.10 — PBP transglycosylase domain-like

Domain ID domain_id	d2olvb2
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 (6 domains)

Domain ID domain_id	2olvA01
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	1310 — Penicillin-binding protein 2a (Domain 2)
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	2olvA02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	3810 — Penicillin binding protein transpeptidase fold
Homologous superfamily homologous superfamily	10 — Biosynthetic peptidoglycan transglycosylase-like

Domain ID domain_id	2olvA03
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	2olvB01
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	1310 — Penicillin-binding protein 2a (Domain 2)
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	2olvB02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	3810 — Penicillin binding protein transpeptidase fold
Homologous superfamily homologous superfamily	10 — Biosynthetic peptidoglycan transglycosylase-like

Domain ID domain_id	2olvB03
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	79.565 Å
Unit-cell length b length_b	212.211 Å
Unit-cell length c length_c	91.635 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 2
Space-group number int_tables_number	18
Crystal system crystal_system	—

Resolution resolution	2.800 Å
Low-resolution limit resolution_low	44.150 Å
R factor r_factor	0.2340
R_work r_work	0.2310
R_free r_free	0.2800

Structural Insight Into the Transglycosylation Step Of Bacterial Cell Wall Biosynthesis : Donor Ligand Complex

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

2olv__assembly_1__model_1

2olv__assembly_1__model_1 | I(q)

2olv__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

6. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (4 domains)

CATH v4.4 (6 domains)

7. Citations (1)

Structural Insight Into the Transglycosylation Step Of Bacterial Cell Wall Biosynthesis : Donor Ligand Complex

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

2olv__assembly_1__model_1

2olv__assembly_1__model_1 | I(q)

2olv__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

6. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (4 domains)

CATH v4.4 (6 domains)

7. Citations (1)