1p4a

Crystal Structure of the PurR complexed with cPRPP

Method: X-RAY DIFFRACTION

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

Pur operon repressor

Bacillus subtilis

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	1-ALPHA-PYROPHOSPHORYL-2-ALPHA,3-ALPHA-DIHYDROXY-4-BETA-CYCLOPENTANE-METHANOL-5-PHOSPHATE × 2 water × 2	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 2	1-ALPHA-PYROPHOSPHORYL-2-ALPHA,3-ALPHA-DIHYDROXY-4-BETA-CYCLOPENTANE-METHANOL-5-PHOSPHATE × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PURR_BACSU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–285； UniProt 1–285 Author chain B； PDBConstruct 1–285； UniProt 1–285 Author chain C； PDBConstruct 1–285； UniProt 1–285 Author chain D； PDBConstruct 1–285； UniProt 1–285

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	1p4a
Deposition date deposition_date	2003-04-22
Structure title title	Crystal Structure of the PurR complexed with cPRPP
Keywords keywords	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.

1p4a__assembly_2__model_1

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

Download this curve (.dat)

1p4a__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1p4a__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	25.13 Å
Rg (electron density)	23.70 Å
Total Rg	24.69 Å
Atom count	4174
Residues	537
Excluded volume	75113 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1p4a__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1p4a__assembly_2__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 (3)

Entity 1 Entity 1 polymer

Description description	Pur operon repressor
Molecular weight formula_weight	31260.9 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	8926

MKFRRSGRLVDLTNYLLTHPHELIPLTFFSERYESAKSSISEDLTIIKQTFEQQGIGTLLTVPGAAGGVKYIPKMKQAEAEEFVQTLGQSLANPERILPGGYVYLTDILGKPSVLSKVGKLFASVFAEREIDVVMTVATKGIPLAYAAASYLNVPVVIVRKDNKVTEGSTVSINYVSGSSNRIQTMSLAKRSMKTGSNVLIIDDFMKAGGTINGMINLLDEFNANVAGIGVLVEAEGVDERLVDEYMSLLTLSTINMKEKSIEIQNGNFLRFFKDNLLKNGETES

Source Source

Source organism organism	Bacillus subtilis
NCBI taxonomy ID ncbi_taxonomy_id	1423
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	1-ALPHA-PYROPHOSPHORYL-2-ALPHA,3-ALPHA-DIHYDROXY-4-BETA-CYCLOPENTANE-METHANOL-5-PHOSPHATE
Molecular weight formula_weight	388.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	574

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6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

Domain ID domain_id	d1p4aa1
Class class	a — All alpha proteins
Fold Fold fold	a.4 — DNA/RNA-binding 3-helical bundle
Superfamily Superfamily superfamily	a.4.5 — 'Winged helix' DNA-binding domain
Family Family family	a.4.5.40 — N-terminal domain of Bacillus PurR

Domain ID domain_id	d1p4aa2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.61 — PRTase-like
Superfamily Superfamily superfamily	c.61.1 — PRTase-like
Family Family family	c.61.1.1 — Phosphoribosyltransferases (PRTases)

Domain ID domain_id	d1p4ab1
Class class	a — All alpha proteins
Fold Fold fold	a.4 — DNA/RNA-binding 3-helical bundle
Superfamily Superfamily superfamily	a.4.5 — 'Winged helix' DNA-binding domain
Family Family family	a.4.5.40 — N-terminal domain of Bacillus PurR

Domain ID domain_id	d1p4ab2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.61 — PRTase-like
Superfamily Superfamily superfamily	c.61.1 — PRTase-like
Family Family family	c.61.1.1 — Phosphoribosyltransferases (PRTases)

Domain ID domain_id	d1p4ac1
Class class	a — All alpha proteins
Fold Fold fold	a.4 — DNA/RNA-binding 3-helical bundle
Superfamily Superfamily superfamily	a.4.5 — 'Winged helix' DNA-binding domain
Family Family family	a.4.5.40 — N-terminal domain of Bacillus PurR

Domain ID domain_id	d1p4ac2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.61 — PRTase-like
Superfamily Superfamily superfamily	c.61.1 — PRTase-like
Family Family family	c.61.1.1 — Phosphoribosyltransferases (PRTases)

Domain ID domain_id	d1p4ad1
Class class	a — All alpha proteins
Fold Fold fold	a.4 — DNA/RNA-binding 3-helical bundle
Superfamily Superfamily superfamily	a.4.5 — 'Winged helix' DNA-binding domain
Family Family family	a.4.5.40 — N-terminal domain of Bacillus PurR

Domain ID domain_id	d1p4ad2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.61 — PRTase-like
Superfamily Superfamily superfamily	c.61.1 — PRTase-like
Family Family family	c.61.1.1 — Phosphoribosyltransferases (PRTases)

CATH v4.4 (8 domains)

Domain ID domain_id	1p4aA01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	10 — Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain

Domain ID domain_id	1p4aA02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	2020 —

Domain ID domain_id	1p4aB01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	10 — Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain

Domain ID domain_id	1p4aB02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	2020 —

Domain ID domain_id	1p4aC01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	10 — Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain

Domain ID domain_id	1p4aC02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	2020 —

Domain ID domain_id	1p4aD01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	10 — Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain

Domain ID domain_id	1p4aD02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	2020 —

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Unit-cell length a length_a	58.371 Å
Unit-cell length b length_b	135.718 Å
Unit-cell length c length_c	82.071 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	95.10 °
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	2.220 Å
Low-resolution limit resolution_low	37.800 Å
R factor r_factor	0.1803
R_work r_work	0.1773
R_free r_free	0.2337

Crystal Structure of the PurR complexed with cPRPP

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

Pur operon repressor

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

1p4a__assembly_2__model_1

1p4a__assembly_2__model_1 | I(q)

1p4a__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 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

CATH v4.4 (8 domains)

7. Citations (1)

Crystal Structure of the PurR complexed with cPRPP

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

Pur operon repressor

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

1p4a__assembly_2__model_1

1p4a__assembly_2__model_1 | I(q)

1p4a__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 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

CATH v4.4 (8 domains)

7. Citations (1)