SAXSdb — 2p5t

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

Putative transcriptional regulator PezA

Streptococcus pneumoniae

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	PezT × 2 （Q97QZ1）	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 5	fragment of PezA helix-turn-helix motif × 1 PezT × 2 （Q97QZ1）	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 4	PezT × 2 （Q97QZ1）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q97QZ2_STRPN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain A； PDBConstruct 1–158； UniProt 1–158 Author chain C； PDBConstruct 1–158； UniProt 1–158 Author chain E； PDBConstruct 1–158； UniProt 1–158 Author chain G； PDBConstruct 1–158； UniProt 1–158

PezT

Streptococcus pneumoniae

UniProt Q97QZ1

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	Putative transcriptional regulator PezA × 2 （Q97QZ2）	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 5	fragment of PezA helix-turn-helix motif × 1 Putative transcriptional regulator PezA × 2 （Q97QZ2）	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 4	Putative transcriptional regulator PezA × 2 （Q97QZ2）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q97QZ1_STRPN
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain B； PDBConstruct 1–253； UniProt 1–253 Author chain D； PDBConstruct 1–253； UniProt 1–253 Author chain F； PDBConstruct 1–253； UniProt 1–253 Author chain H； PDBConstruct 1–253； UniProt 1–253

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	2p5t
Deposition date deposition_date	2007-03-16
Structure title title	Molecular and structural characterization of the PezAT chromosomal toxin-antitoxin system of the human pathogen Streptococcus pneumoniae
Keywords keywords	postsegregational killing system, phosphoryltransferase, helix-turn-helix motif, TRANSCRIPTION REGULATOR; TRANSCRIPTION REGULATOR
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.

2p5t__assembly_3__model_1

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

Download this curve (.dat)

2p5t__assembly_3__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2p5t__assembly_3__model_1 | P(r) · Pending

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

Rg（Guinier）	30.49 Å
Rg (electron density)	29.93 Å
Total Rg	30.58 Å
Atom count	5454
Residues	670
Excluded volume	97387 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2p5t__assembly_1__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2p5t__assembly_2__model_1`	pentameric （5）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`2p5t__assembly_3__model_1`	tetrameric （4）	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	fragment of PezA helix-turn-helix motif
Molecular weight formula_weight	2826.5 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	X
Atom count atom_count	11093

XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX

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	Putative transcriptional regulator PezA
Molecular weight formula_weight	18267.7 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C,E,G

MIGKNIKSLRKTHDLTQLEFARIVGISRNSLSRYENGTSSVSTELIDIICQKFNVSYVDIVGEDKMLNPVEDYELTLKIEIVKERGANLLSRLYRYQDSQGISIDDESNPWILMSDDLSDLIHTNIYLVETFDEIERYSGYLDGIERMLEISEKRMVA

Source Source

Source organism organism	Streptococcus pneumoniae
NCBI taxonomy ID ncbi_taxonomy_id	170187
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 polymer

Description description	PezT
Molecular weight formula_weight	29106.1 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,D,F,H

MEIQDYTDSEFKHALARNLRSLTRGKKSSKQPIAILLGGQSGAGKTTIHRIKQKEFQGNIVIIDGDSFRSQHPHYLELQQEYGKDSVEYTKDFAGKMVESLVTKLSSLGYNLLIEGTLRTVDVPKKTAQLLKNKGYEVQLALIATKPELSYLSTLIRYEELYIINPNQARATPKEHHDFIVNHLVDNTRKLEELAIFERIQIYQRDRSCVYDSKENTTSAADVLQELFFGEWSQVEKEMLQVGEKRLNELLEK

Source Source

Source organism organism	Streptococcus pneumoniae
NCBI taxonomy ID ncbi_taxonomy_id	1313
Host organism host_organism	Escherichia coli

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6. Fold Classification (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

Domain ID domain_id	2p5tA00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	8 — Helicase, Ruva Protein; domain 3
Homologous superfamily homologous superfamily	130 —

Domain ID domain_id	2p5tB00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	2p5tC00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	8 — Helicase, Ruva Protein; domain 3
Homologous superfamily homologous superfamily	130 —

Domain ID domain_id	2p5tD00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	2p5tE00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	8 — Helicase, Ruva Protein; domain 3
Homologous superfamily homologous superfamily	130 —

Domain ID domain_id	2p5tF00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	2p5tG00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	8 — Helicase, Ruva Protein; domain 3
Homologous superfamily homologous superfamily	130 —

Domain ID domain_id	2p5tH00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

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Unit-cell length a length_a	80.520 Å
Unit-cell length b length_b	102.860 Å
Unit-cell length c length_c	254.440 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	3.200 Å
Low-resolution limit resolution_low	47.670 Å
R factor r_factor	0.2169
R_work r_work	0.2137
R_free r_free	0.2773

Molecular and structural characterization of the PezAT chromosomal toxin-antitoxin system of the human pathogen Streptococcus pneumoniae

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

Putative transcriptional regulator PezA

State in the Current Structure

Other States of the Same Protein in the Database

PezT

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

2p5t__assembly_3__model_1

2p5t__assembly_3__model_1 | I(q)

2p5t__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

6. Fold Classification (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

7. Citations (1)

Molecular and structural characterization of the PezAT chromosomal toxin-antitoxin system of the human pathogen Streptococcus pneumoniae

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

Putative transcriptional regulator PezA

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

PezT

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

2p5t__assembly_3__model_1

2p5t__assembly_3__model_1 | I(q)

2p5t__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

6. Fold Classification (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

7. Citations (1)