SAXSdb — 1zme

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

PROLINE UTILIZATION TRANSCRIPTION ACTIVATOR

Saccharomyces cerevisiae

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(APCPGPGPGPAPAPGPCPCPAPAPCPTPCPCPG)-3') ; × 1 ;DNA (5'-D(APCPGPGPAPGP(5IU)PTPGPGPCPTP(5IU)PCPCPCPG)-3') ; × 1 ZINC ION × 4 water × 4	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PUT3_YEAST
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 1–70； UniProt 31–100 Author chain D； PDBConstruct 1–70； UniProt 31–100

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	1zme
Deposition date deposition_date	1997-08-06
Structure title title	CRYSTAL STRUCTURE OF PUT3/DNA COMPLEX
Keywords keywords	COMPLEX (TRANSCRIPTION REGULATION-DNA), PUT3, ZN2CYS6, BINUCLEAR CLUSTER, TRANSCRIPTION FACTOR, TRANSCRIPTION-DNA COMPLEX; TRANSCRIPTION/DNA
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.

1zme__assembly_1__model_1

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

Download this curve (.dat)

1zme__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1zme__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	23.73 Å
Rg (electron density)	24.12 Å
Total Rg	24.57 Å
Atom count	1800
Residues	172
Excluded volume	29984 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1zme__assembly_1__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 (5)

Entity 1 Entity 1 polymer

Description description	;DNA (5'-D(APCPGPGPGPAPAPGPCPCPAPAPCPTPCPCP*G)-3') ;
Molecular weight formula_weight	5206.4 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	A
Atom count atom_count	1957

ACGGGAAGCCAACTCCG

Source Source

Source organism organism	Saccharomyces cerevisiae
Common name common_name	;baker's yeast ;
NCBI taxonomy ID ncbi_taxonomy_id	4932
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	;DNA (5'-D(APCPGPGPAPGP(5IU)PTPGPGPCPTP(5IU)PCPCPCP*G)-3') ;
Molecular weight formula_weight	5443.1 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	B

ACGGAGUTGGCTUCCCG

Entity 3 Entity 3 polymer

Description description	PROLINE UTILIZATION TRANSCRIPTION ACTIVATOR
Molecular weight formula_weight	7963.3 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,D

SVACLSCRKRHIKCPGGNPCQKCVTSNAICEYLEPSKKIVVSTKYLQQLQKDLNDKTEENNRLKALLLER

Source Source

Source organism organism	Saccharomyces cerevisiae
Common name common_name	;baker's yeast ;
NCBI taxonomy ID ncbi_taxonomy_id	4932
Host organism host_organism	Escherichia coli

Entity 4 Entity 4 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	157

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6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d1zmec1
Class class	g — Small proteins
Fold Fold fold	g.38 — Zn2/Cys6 DNA-binding domain
Superfamily Superfamily superfamily	g.38.1 — Zn2/Cys6 DNA-binding domain
Family Family family	g.38.1.1 — Zn2/Cys6 DNA-binding domain

Domain ID domain_id	d1zmec2
Class class	h — Coiled coil proteins
Fold Fold fold	h.1 — Parallel coiled-coil
Superfamily Superfamily superfamily	h.1.3 — Leucine zipper domain
Family Family family	h.1.3.1 — Leucine zipper domain

Domain ID domain_id	d1zmed1
Class class	g — Small proteins
Fold Fold fold	g.38 — Zn2/Cys6 DNA-binding domain
Superfamily Superfamily superfamily	g.38.1 — Zn2/Cys6 DNA-binding domain
Family Family family	g.38.1.1 — Zn2/Cys6 DNA-binding domain

Domain ID domain_id	d1zmed2
Class class	h — Coiled coil proteins
Fold Fold fold	h.1 — Parallel coiled-coil
Superfamily Superfamily superfamily	h.1.3 — Leucine zipper domain
Family Family family	h.1.3.1 — Leucine zipper domain

CATH v4.4 (4 domains)

Domain ID domain_id	1zmeC01
Class class	4 — Few Secondary Structures
Architecture architecture	10 — Irregular
Topology topology	240 — CD2-Gal4
Homologous superfamily homologous superfamily	10 — Zn(2)-C6 fungal-type DNA-binding domain

Domain ID domain_id	1zmeC02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	460 — Single helix bin

Domain ID domain_id	1zmeD01
Class class	4 — Few Secondary Structures
Architecture architecture	10 — Irregular
Topology topology	240 — CD2-Gal4
Homologous superfamily homologous superfamily	10 — Zn(2)-C6 fungal-type DNA-binding domain

Domain ID domain_id	1zmeD02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	460 — Single helix bin

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Unit-cell length a length_a	121.650 Å
Unit-cell length b length_b	121.650 Å
Unit-cell length c length_c	39.100 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	12

Space group space_group	P 6
Space-group number int_tables_number	168
Crystal system crystal_system	—

Resolution resolution	2.500 Å
Low-resolution limit resolution_low	8.000 Å
R factor r_factor	0.2080
R_work r_work	0.2080
R_free r_free	0.2920

CRYSTAL STRUCTURE OF PUT3/DNA COMPLEX

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

PROLINE UTILIZATION TRANSCRIPTION ACTIVATOR

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

1zme__assembly_1__model_1

1zme__assembly_1__model_1 | I(q)

1zme__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

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)

CRYSTAL STRUCTURE OF PUT3/DNA COMPLEX

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

PROLINE UTILIZATION TRANSCRIPTION ACTIVATOR

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

1zme__assembly_1__model_1

1zme__assembly_1__model_1 | I(q)

1zme__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

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)