SAXSdb — 3c7j

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

Transcriptional regulator, GntR family

Pseudomonas syringae pv. tomato

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 4	NICKEL (II) ION × 4 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q87U60_PSESM
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–237； UniProt 1–234 Author chain B； PDBConstruct 4–237； UniProt 1–234

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	3c7j
Deposition date deposition_date	2008-02-07
Structure title title	Crystal structure of transcriptional regulator (GntR family member) from Pseudomonas syringae pv. tomato str. DC3000
Keywords keywords	;transcriptional regulator, GntR family, structural genomics, MCSG, PSI-2, Protein Structure Initiative, Midwest Center for Structural Genomics, DNA-binding, Transcription regulation, TRANSCRIPTION REGULATOR ;; TRANSCRIPTION REGULATOR
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.

3c7j__assembly_1__model_1

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

Download this curve (.dat)

3c7j__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3c7j__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	38.15 Å
Rg (electron density)	37.91 Å
Total Rg	38.18 Å
Atom count	7328
Residues	908
Excluded volume	130420 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3c7j__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 (3)

Entity 1 Entity 1 polymer

Description description	Transcriptional regulator, GntR family
Molecular weight formula_weight	26792.7 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	4037

SNAMRKSDREAFLSSVLGNEQPPAHLARTVIEEKLRNAIIDGSLPSGTALRQQELATLFGVSRMPVREALRQLEAQSLLRVETHKGAVVAPLITEDAVDAYALRILLESEALRLSIPLLDADDLAAAASYIEQLEVETDFGQIGRLNRMFHLSLYAKTHNKRLMRLVEEGLNEEERFLRFNLSSMGLGKLSQDDHWQLLRLAEQKAVEPCVEALQYHLNRGVQAVTQYLQSQKAGNV

Source Source

Source organism organism	Pseudomonas syringae pv. tomato
NCBI taxonomy ID ncbi_taxonomy_id	223283
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	NICKEL (II) ION
Molecular weight formula_weight	58.7 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	354

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6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id	3c7jA01
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	3c7jA02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
Homologous superfamily homologous superfamily	530 — GntR ligand-binding domain-like

Domain ID domain_id	3c7jB01
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	3c7jB02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
Homologous superfamily homologous superfamily	530 — GntR ligand-binding domain-like

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Unit-cell length a length_a	55.954 Å
Unit-cell length b length_b	132.768 Å
Unit-cell length c length_c	170.461 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	C 2 2 21
Space-group number int_tables_number	20
Crystal system crystal_system	—

Resolution resolution	2.100 Å
Low-resolution limit resolution_low	45.000 Å
R factor r_factor	0.1820
R_work r_work	0.1800
R_free r_free	0.2270

Crystal structure of transcriptional regulator (GntR family member) from Pseudomonas syringae pv. tomato str. DC3000

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

Transcriptional regulator, GntR family

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

3c7j__assembly_1__model_1

3c7j__assembly_1__model_1 | I(q)

3c7j__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 (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) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)

Crystal structure of transcriptional regulator (GntR family member) from Pseudomonas syringae pv. tomato str. DC3000

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

Transcriptional regulator, GntR family

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

3c7j__assembly_1__model_1

3c7j__assembly_1__model_1 | I(q)

3c7j__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 (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) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)