SAXSdb — 3dnv

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

Protein hipA

Escherichia coli

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 4 DNA 2	HTH-type transcriptional regulator hipB × 2 （P23873） ;DNA (5'-D(DAPDCPDTPDAPDTPDCPDCPDCPDCPDTPDTPDAPDAPDGPDGPDGPDGPDAPDTPDAP*DG)-3') ; × 2 SULFATE ION × 16 water × 6	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	HIPA_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–440； UniProt 1–440

HTH-type transcriptional regulator hipB

Escherichia coli

UniProt P23873

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 4 DNA 2	Protein hipA × 2 （P23874） ;DNA (5'-D(DAPDCPDTPDAPDTPDCPDCPDCPDCPDTPDTPDAPDAPDGPDGPDGPDGPDAPDTPDAP*DG)-3') ; × 2 SULFATE ION × 16 water × 6	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	HIPB_ECOLI
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–88； UniProt 1–88

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	3dnv
Deposition date deposition_date	2008-07-02
Structure title title	MDT Protein
Keywords keywords	persistence, mdt, DNA-binding, Repressor, Transcription, Transcription regulation, 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.

3dnv__assembly_1__model_1

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

Download this curve (.dat)

3dnv__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3dnv__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	35.80 Å
Rg (electron density)	36.14 Å
Total Rg	36.34 Å
Atom count	8612
Residues	1008
Excluded volume	151210 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3dnv__assembly_1__model_1`	hexameric （6）	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	Protein hipA
Molecular weight formula_weight	49444.5 kDa
Mutation mutation	D309Q
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	4340

MPKLVTWMNNQRVGELTKLANGAHTFKYAPEWLASRYARPLSLSLPLQRGNITSDAVFNFFDNLLPDSPIVRDRIVKRYHAKSRQPFDLLSEIGRDSVGAVTLIPEDETVTHPIMAWEKLTEARLEEVLTAYKADIPLGMIREENDFRISVAGAQEKTALLRIGNDWCIPKGITPTTHIIKLPIGEIRQPNATLDLSQSVDNEYYCLLLAKELGLNVPDAEIIKAGNVRALAVERFDRRWNAERTVLLRLPQEDMCQTFGLPSSVKYESDGGPGIARIMAFLMGSSEALKDRYDFMKFQVFQWLIGATQGHAKNFSVFIQAGGSYRLTPFYDIISAFPVLGGTGIHISDLKLAMGLNASKGKKTAIDKIYPRHFLATAKVLRFPEVQMHEILSDFARMIPAALDNVKTSLPTDFPENVVTAVESNVLRLHGRLSREYGSK

Source Source

Source organism organism	Escherichia coli
NCBI taxonomy ID ncbi_taxonomy_id	83333
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	HTH-type transcriptional regulator hipB
Molecular weight formula_weight	10024.3 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

MMSFQKIYSPTQLANAMKLVRQQNGWTQSELAKKIGIKQATISNFENNPDNTTLTTFFKILQSLELSMTLCDAKNASPESTEQQNLEW

Source Source

Source organism organism	Escherichia coli
NCBI taxonomy ID ncbi_taxonomy_id	83333
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 polymer

Description description	;DNA (5'-D(DAPDCPDTPDAPDTPDCPDCPDCPDCPDTPDTPDAPDAPDGPDGPDGPDGPDAPDTPDAP*DG)-3') ;
Molecular weight formula_weight	6447.2 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	T

ACTATCCCCTTAAGGGGATAG

Entity 4 Entity 4 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	8

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	34

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6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d3dnva_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.144 — Protein kinase-like (PK-like)
Superfamily Superfamily superfamily	d.144.1 — Protein kinase-like (PK-like)
Family Family family	d.144.1.7 — Protein kinases, catalytic subunit

CATH v4.4 (1 domains)

Domain ID domain_id	3dnvB00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	260 — 434 Repressor (Amino-terminal Domain)
Homologous superfamily homologous superfamily	40 — lambda repressor-like DNA-binding domains

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Unit-cell length a length_a	166.340 Å
Unit-cell length b length_b	166.340 Å
Unit-cell length c length_c	62.090 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	8

Space group space_group	P 4 2 2
Space-group number int_tables_number	89
Crystal system crystal_system	—

Resolution resolution	2.680 Å
Low-resolution limit resolution_low	58.170 Å
R factor r_factor	0.2280
R_work r_work	0.2280
R_free r_free	0.2850

MDT Protein

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

Protein hipA

State in the Current Structure

Other States of the Same Protein in the Database

HTH-type transcriptional regulator hipB

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

3dnv__assembly_1__model_1

3dnv__assembly_1__model_1 | I(q)

3dnv__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

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

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)

MDT Protein

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

Protein hipA

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

HTH-type transcriptional regulator hipB

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

3dnv__assembly_1__model_1

3dnv__assembly_1__model_1 | I(q)

3dnv__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

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

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)