SAXSdb — 3bku

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

Nickel-responsive regulator

Escherichia coli

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 4	water × 4	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 2	water × 2	Consistent with protein count
3	Protein homooligomer	Homooligomer	Protein 2	water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	NIKR_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–86； UniProt 48–133 Author chain B； PDBConstruct 1–86； UniProt 48–133 Author chain C； PDBConstruct 1–86； UniProt 48–133 Author chain D； PDBConstruct 1–86； UniProt 48–133

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	3bku
Deposition date deposition_date	2007-12-07
Structure title title	Apo C-terminal Domain of NikR
Keywords keywords	;NikR, nickel regulatory protein, transcription factor, beta sandwich, DNA-binding, Metal-binding, Repressor, Transcription regulation, METAL BINDING PROTEIN ;; METAL 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.

3bku__assembly_1__model_1

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

Download this curve (.dat)

3bku__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3bku__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	19.83 Å
Rg (electron density)	18.27 Å
Total Rg	19.12 Å
Atom count	2218
Residues	299
Excluded volume	38563 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3bku__assembly_1__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3bku__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`3bku__assembly_3__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 (2)

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6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d3bkua_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.58 — Ferredoxin-like
Superfamily Superfamily superfamily	d.58.18 — ACT-like
Family Family family	d.58.18.4 — Nickel responsive regulator NikR, C-terminal domain

Domain ID domain_id	d3bkub_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.58 — Ferredoxin-like
Superfamily Superfamily superfamily	d.58.18 — ACT-like
Family Family family	d.58.18.4 — Nickel responsive regulator NikR, C-terminal domain

Domain ID domain_id	d3bkuc_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.58 — Ferredoxin-like
Superfamily Superfamily superfamily	d.58.18 — ACT-like
Family Family family	d.58.18.4 — Nickel responsive regulator NikR, C-terminal domain

Domain ID domain_id	d3bkud_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.58 — Ferredoxin-like
Superfamily Superfamily superfamily	d.58.18 — ACT-like
Family Family family	d.58.18.4 — Nickel responsive regulator NikR, C-terminal domain

CATH v4.4 (4 domains)

Domain ID domain_id	3bkuA00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	1150 — ACT-like. Chain A, domain 2

Domain ID domain_id	3bkuB00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	1150 — ACT-like. Chain A, domain 2

Domain ID domain_id	3bkuC00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	1150 — ACT-like. Chain A, domain 2

Domain ID domain_id	3bkuD00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	1150 — ACT-like. Chain A, domain 2

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Unit-cell length a length_a	67.350 Å
Unit-cell length b length_b	59.660 Å
Unit-cell length c length_c	75.140 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	94.01 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	16

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	2.100 Å
Low-resolution limit resolution_low	50.000 Å
R factor r_factor	0.2910
R_work r_work	0.2880
R_free r_free	0.3360

Description description	Nickel-responsive regulator
Molecular weight formula_weight	9724.8 kDa
Source method src_method	man
Copy count entity_count	4

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	2233

Apo C-terminal Domain of NikR

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

Nickel-responsive 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

3bku__assembly_1__model_1

3bku__assembly_1__model_1 | I(q)

3bku__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 water

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)

Source organism organism	Escherichia coli
NCBI taxonomy ID ncbi_taxonomy_id	562
Host organism host_organism	Escherichia coli BL21(DE3)

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	15

Apo C-terminal Domain of NikR

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

Nickel-responsive 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

3bku__assembly_1__model_1

3bku__assembly_1__model_1 | I(q)

3bku__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 water

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)