SAXSdb — 3d6w

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

Methyl-accepting/DNA response regulator

Bacillus cereus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 4	MAGNESIUM ION × 4 1,2-ETHANEDIOL × 2 FORMIC ACID × 4 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q73A38_BACC1
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–109； UniProt 106–214 Author chain B； PDBConstruct 1–109； UniProt 106–214

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	3d6w
Deposition date deposition_date	2008-05-20
Structure title title	LytTr DNA-binding domain of putative methyl-accepting/DNA response regulator from Bacillus cereus.
Keywords keywords	;structural genomics, APC7590, LytTr DNA-binding domain, methyl-accepting/DNA response regulator, PSI-2, Protein Structure Initiative, Midwest Center for Structural Genomics, MCSG, DNA BINDING PROTEIN ;; DNA BINDING PROTEIN
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.

3d6w__assembly_1__model_1

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

Download this curve (.dat)

3d6w__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3d6w__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	26.79 Å
Rg (electron density)	25.62 Å
Total Rg	26.40 Å
Atom count	3580
Residues	428
Excluded volume	64497 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3d6w__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	Methyl-accepting/DNA response regulator
Molecular weight formula_weight	12840.4 kDa
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	1866

GKSVVTLKTTDGWIPVPFSKVMYLEAKDKKTYVNAEELTGTHKYSLQEFEYLLPKDSFIRCHRSFIVNVNHIKAIYPDTHSTFLLSMDNGERVPVSQSYASYFRKLLGFGS

Source Source

Source organism organism	Bacillus cereus
NCBI taxonomy ID ncbi_taxonomy_id	222523
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	FORMIC ACID
Molecular weight formula_weight	46.0 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	76

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6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id	3d6wA01
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily	40 —

Domain ID domain_id	3d6wA02
Class class	2 — Mainly Beta
Architecture architecture	20 — Single Sheet
Topology topology	25 — N-terminal domain of TfIIb
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	3d6wB01
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily	40 —

Domain ID domain_id	3d6wB02
Class class	2 — Mainly Beta
Architecture architecture	20 — Single Sheet
Topology topology	25 — N-terminal domain of TfIIb
Homologous superfamily homologous superfamily	10 —

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Unit-cell length a length_a	88.784 Å
Unit-cell length b length_b	88.784 Å
Unit-cell length c length_c	74.425 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	16

Space group space_group	P 42 2 2
Space-group number int_tables_number	93
Crystal system crystal_system	—

Resolution resolution	2.400 Å
Low-resolution limit resolution_low	48.000 Å
R factor r_factor	0.1840
R_work r_work	0.1820
R_free r_free	0.2090

LytTr DNA-binding domain of putative methyl-accepting/DNA response regulator from Bacillus cereus.

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

Methyl-accepting/DNA response regulator

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

3d6w__assembly_1__model_1

3d6w__assembly_1__model_1 | I(q)

3d6w__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 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)

LytTr DNA-binding domain of putative methyl-accepting/DNA response regulator from Bacillus cereus.

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

Methyl-accepting/DNA response regulator

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

3d6w__assembly_1__model_1

3d6w__assembly_1__model_1 | I(q)

3d6w__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 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)