SAXSdb — 4zm2

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

Antitoxin phd

Enterobacteria phage P1

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Homooligomer	Protein 2 DNA 2	;DNA (5'-D(GPCPTPTPGPTPGPTPAPCPAPCPAPT)-3') ; × 1 ;DNA (5'-D(CPAPTPGPTPGPTPAPCPAPCPAPAPG)-3') ; × 1	Consistent with all polymers
2	Protein–DNA	Homooligomer	Protein 2 DNA 2	;DNA (5'-D(GPCPTPTPGPTPGPTPAPCPAPCPAPT)-3') ; × 1 ;DNA (5'-D(CPAPTPGPTPGPTPAPCPAPCPAPAPG)-3') ; × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PHD_BPP1
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–73； UniProt 1–73 Author chain B； PDBConstruct 1–73； UniProt 1–73 Author chain C； PDBConstruct 1–73； UniProt 1–73 Author chain D； PDBConstruct 1–73； UniProt 1–73

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	4zm2
Deposition date deposition_date	2015-05-02
Structure title title	Antitoxin Phd from phage P1 in complex with its operator DNA inverted repeat in a monoclinic space group
Keywords keywords	;transcription factor, toxin-antitoxin, DNA binding, intrinsic disorder, conditional cooperativity, protein-DNA complex, transcription ;; TRANSCRIPTION
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.

4zm2__assembly_2__model_1

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

Download this curve (.dat)

4zm2__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4zm2__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	18.38 Å
Rg (electron density)	17.45 Å
Total Rg	18.24 Å
Atom count	1378
Residues	136
Excluded volume	22469 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4zm2__assembly_1__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`4zm2__assembly_2__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	Antitoxin phd
Molecular weight formula_weight	8143.1 kDa
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	2743

MQSINFRTARGNLSEVLNNVEAGEEVEITRRGREPAVIVSKATFEAYKKAALDAEFASLFDTLDSTNKELVNR

Source Source

Source organism organism	Enterobacteria phage P1
NCBI taxonomy ID ncbi_taxonomy_id	10678
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 polymer

Description description	;DNA (5'-D(GPCPTPTPGPTPGPTPAPCPAPCPAP*T)-3') ;
Molecular weight formula_weight	4270.8 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	E,G

GCTTGTGTACACAT

Entity 3 Entity 3 polymer

Description description	;DNA (5'-D(CPAPTPGPTPGPTPAPCPAPCPAPAP*G)-3') ;
Molecular weight formula_weight	4288.8 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	F,H

CATGTGTACACAAG

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6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id	4zm2A00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1620 — YefM-like fold
Homologous superfamily homologous superfamily	10 — YefM-like domain

Domain ID domain_id	4zm2B01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1620 — YefM-like fold
Homologous superfamily homologous superfamily	10 — YefM-like domain

Domain ID domain_id	4zm2C00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1620 — YefM-like fold
Homologous superfamily homologous superfamily	10 — YefM-like domain

Domain ID domain_id	4zm2D00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1620 — YefM-like fold
Homologous superfamily homologous superfamily	10 — YefM-like domain

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Unit-cell length a length_a	65.870 Å
Unit-cell length b length_b	56.580 Å
Unit-cell length c length_c	74.840 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	111.47 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	3.880 Å
Low-resolution limit resolution_low	43.920 Å
R factor r_factor	0.2620
R_work r_work	0.2615
R_free r_free	0.2709

Antitoxin Phd from phage P1 in complex with its operator DNA inverted repeat in a monoclinic space group

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

Antitoxin phd

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

4zm2__assembly_2__model_1

4zm2__assembly_2__model_1 | I(q)

4zm2__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 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)

Antitoxin Phd from phage P1 in complex with its operator DNA inverted repeat in a monoclinic space group

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

Antitoxin phd

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

4zm2__assembly_2__model_1

4zm2__assembly_2__model_1 | I(q)

4zm2__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 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)