SAXSdb — 1pp7

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

39 kDa initiator binding protein

Trichomonas vaginalis

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Monomer	Protein 1 DNA 2	FERREDOXIN INR × 1 FERREDOXIN INR × 1 ZINC ION × 7 water × 3	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q95VR4_TRIVA
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain U； PDBConstruct 1–126； UniProt 1–126

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	1pp7
Deposition date deposition_date	2003-06-16
Structure title title	Crystal structure of the T. vaginalis Initiator binding protein bound to the ferredoxin Inr
Keywords keywords	Initiator, core promoter, transcription initation, IBP39, T. vaginalis, 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.

1pp7__assembly_1__model_1

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

Download this curve (.dat)

1pp7__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1pp7__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	17.52 Å
Rg (electron density)	16.34 Å
Total Rg	17.30 Å
Atom count	1440
Residues	139
Excluded volume	24230 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1pp7__assembly_1__model_1`	trimeric （3）	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	FERREDOXIN INR
Molecular weight formula_weight	3932.6 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	E
Atom count atom_count	1505

GGTTACTTCACTT

Entity 2 Entity 2 polymer

Description description	FERREDOXIN INR
Molecular weight formula_weight	4008.7 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	F

CAAGTGAAGTAAC

Entity 3 Entity 3 polymer

Description description	39 kDa initiator binding protein
Molecular weight formula_weight	15206.2 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	U

MDSNDLEASFTSRLPPEIVAALKRKSSRDPNSRFPRKLHMLLTYLASNPQLEEEIGLSWISDTEFKMKKKNVALVMGIKLNTLNVNLRDLAFEQLQHDKGGWTQWKRSGFTRNSVFEDPTQNDSPMHHHHH

Source Source

Source organism organism	Trichomonas vaginalis
NCBI taxonomy ID ncbi_taxonomy_id	5722
Host organism host_organism	Escherichia coli BL21(DE3)

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	7

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	65

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6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1pp7u_
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.4.5.44 — 39 kda initiator binding protein, IBP39, N-terminal domain

CATH v4.4 (1 domains)

Domain ID domain_id	1pp7U00
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

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Unit-cell length a length_a	81.340 Å
Unit-cell length b length_b	41.430 Å
Unit-cell length c length_c	58.390 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	4

Space group space_group	P 21 21 2
Space-group number int_tables_number	18
Crystal system crystal_system	—

Resolution resolution	2.450 Å
Low-resolution limit resolution_low	47.430 Å
R factor r_factor	0.1970
R_work r_work	0.1970
R_free r_free	0.2460

Crystal structure of the T. vaginalis Initiator binding protein bound to the ferredoxin Inr

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

39 kDa initiator binding protein

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

1pp7__assembly_1__model_1

1pp7__assembly_1__model_1 | I(q)

1pp7__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

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) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

7. Citations (1)

Crystal structure of the T. vaginalis Initiator binding protein bound to the ferredoxin Inr

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

39 kDa initiator binding protein

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

1pp7__assembly_1__model_1

1pp7__assembly_1__model_1 | I(q)

1pp7__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

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) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

7. Citations (1)