SAXSdb — 3e6b

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

Cyclic nucleotide-binding protein

Desulfitobacterium hafniense

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	(3-CHLORO-4-HYDROXYPHENYL)ACETIC ACID × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q18R04_DESHD
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–232； UniProt 1–232 Author chain B； PDBConstruct 1–232； UniProt 1–232

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	3e6b
Deposition date deposition_date	2008-08-15
Structure title title	OCPA complexed CprK (C200S)
Keywords keywords	CprK, Halorespiration, transcriptional regulator, TRANSCRIPTION REGULATION; TRANSCRIPTION REGULATION
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.

3e6b__assembly_1__model_1

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

Download this curve (.dat)

3e6b__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3e6b__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	26.22 Å
Rg (electron density)	25.29 Å
Total Rg	26.17 Å
Atom count	3364
Residues	416
Excluded volume	60828 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3e6b__assembly_1__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	Cyclic nucleotide-binding protein
Molecular weight formula_weight	28379.6 kDa
Mutation mutation	C200S
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	3639

MSVEGLGKDFCGAIIPDNFFPIEKLRNYTQMGLIRDFAKGSAVIMPGEEITSMIFLVEGKIKLDIIFEDGSEKLLYYAGGNSLIGKLYPTGNNIYATAMEPTRTCWFSEKSLRTVFRTDEDMIFEIFKNYLTKVAYYARQVAEMNTYNPTIRILRLFYELCSSQGKRVGDTYEITMPLSQKSIGEITGVHHVTVSRVLASLKRENILDKKKNKIIVYNLGELKHLSEQTSYYSDPNSSSVDKLAAALDHH

Source Source

Source organism organism	Desulfitobacterium hafniense
NCBI taxonomy ID ncbi_taxonomy_id	272564
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	(3-CHLORO-4-HYDROXYPHENYL)ACETIC ACID
Molecular weight formula_weight	186.6 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	275

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6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d3e6ba1
Class class	b — All beta proteins
Fold Fold fold	b.82 — Double-stranded beta-helix
Superfamily Superfamily superfamily	b.82.3 — cAMP-binding domain-like
Family Family family	b.82.3.2 — cAMP-binding domain

Domain ID domain_id	d3e6ba2
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.4.5.4 — CAP C-terminal domain-like

Domain ID domain_id	d3e6bb1
Class class	b — All beta proteins
Fold Fold fold	b.82 — Double-stranded beta-helix
Superfamily Superfamily superfamily	b.82.3 — cAMP-binding domain-like
Family Family family	b.82.3.2 — cAMP-binding domain

Domain ID domain_id	d3e6bb2
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.4.5.4 — CAP C-terminal domain-like

CATH v4.4 (4 domains)

Domain ID domain_id	3e6bA01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	10 — Jelly Rolls

Domain ID domain_id	3e6bA02
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	3e6bB01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	10 — Jelly Rolls

Domain ID domain_id	3e6bB02
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	42.500 Å
Unit-cell length b length_b	86.510 Å
Unit-cell length c length_c	125.230 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 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.010 Å
Low-resolution limit resolution_low	40.260 Å
R factor r_factor	0.1910
R_work r_work	0.1890
R_free r_free	0.2320

OCPA complexed CprK (C200S)

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

Cyclic nucleotide-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

3e6b__assembly_1__model_1

3e6b__assembly_1__model_1 | I(q)

3e6b__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

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) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)

OCPA complexed CprK (C200S)

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

Cyclic nucleotide-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

3e6b__assembly_1__model_1

3e6b__assembly_1__model_1 | I(q)

3e6b__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

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) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)