SAXSdb — 2v2f

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

PENICILLIN BINDING PROTEIN 1A

STREPTOCOCCUS PNEUMONIAE

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	BARIUM ION × 1 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q9RET4_STRPN
Isoform	—
PDB entities	1, 2
Chains and sequence ranges	Author chain A； PDBConstruct 1–24； UniProt 47–70 Author chain F； PDBConstruct 1–390； UniProt 264–653

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	2v2f
Deposition date deposition_date	2007-06-05
Structure title title	Crystal structure of PBP1a from drug-resistant strain 5204 from Streptococcus pneumoniae
Keywords keywords	TRANSPEPTIDASE ACTIVITY, PEPTIDOGLYCAN SYNTHESIS, TRANSFERASE, HYDROLASE; 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.

2v2f__assembly_1__model_1

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

Download this curve (.dat)

2v2f__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2v2f__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	21.39 Å
Rg (electron density)	20.52 Å
Total Rg	21.28 Å
Atom count	2998
Residues	383
Excluded volume	52986 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2v2f__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 (5)

Entity 1 Entity 1 polymer

Description description	PENICILLIN BINDING PROTEIN 1A
Molecular weight formula_weight	2639.9 kDa
EC 编号 ec_number	2.4.1.129
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	3201

LVATTSSKIYDNKNQLIADLGSER

Source Source

Source organism organism	STREPTOCOCCUS PNEUMONIAE
NCBI taxonomy ID ncbi_taxonomy_id	1313
Host organism host_organism	ESCHERICHIA COLI

Entity 2 Entity 2 polymer

Description description	PENICILLIN BINDING PROTEIN 1A
Molecular weight formula_weight	43432.0 kDa
EC 编号 ec_number	3.4.16.4
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	F

SASNYPAYMDNYLKEVINQVEQETGYNLLTTGMDVYTNVDQEAQKHLWDIYNSDQYVSYPDDDLQVASTVVDVSNGKVIAQLGARHQASNVSFGTNQAVETNRDWGSAMKPITDYAPAIEYGVYDSTATMVNDIPYNYPGTSTPVYNWDRAYFGNITLQYALQQSRNVTAVETLNKVGLDRAKTFLNGLGIDYPSMHYANAISSNTTESNKQYGASSEKMAAAYAAFANGGIYHKPMYINKVVFSDGSKKEFSDVGTRAMKETTAYMMTEMMKTVLAYGTGRGAYLPWLAQAGKTGTSNYTDDEIEKHIKNTGYVAPDEMFVGYTRKYSMAVWTGYSNRLTPIVGDGFLVAAKVYRSMITYLSEGSNPEDWNIPEGLYRNGEFVFKNGAR

Source Source

Source organism organism	STREPTOCOCCUS PNEUMONIAE
NCBI taxonomy ID ncbi_taxonomy_id	1313
Host organism host_organism	ESCHERICHIA COLI

Entity 3 Entity 3 non-polymer

Description description	BARIUM ION
Molecular weight formula_weight	137.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	2-(N-MORPHOLINO)-ETHANESULFONIC ACID
Molecular weight formula_weight	195.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	203

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6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d2v2ff_
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 (1 domains)

Domain ID domain_id	2v2fF00
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	122.960 Å
Unit-cell length b length_b	67.030 Å
Unit-cell length c length_c	49.130 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	100.89 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	1.900 Å
Low-resolution limit resolution_low	19.740 Å
R factor r_factor	0.2130
R_work r_work	0.2100
R_free r_free	0.2460

Crystal structure of PBP1a from drug-resistant strain 5204 from Streptococcus pneumoniae

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

PENICILLIN BINDING PROTEIN 1A

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

2v2f__assembly_1__model_1

2v2f__assembly_1__model_1 | I(q)

2v2f__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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

7. Citations (1)

Crystal structure of PBP1a from drug-resistant strain 5204 from Streptococcus pneumoniae

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

PENICILLIN BINDING PROTEIN 1A

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

2v2f__assembly_1__model_1

2v2f__assembly_1__model_1 | I(q)

2v2f__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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

7. Citations (1)