3qsi

Nickel binding domain of NikR from Helicobacter pylori disclosing partial metal occupancy

Method: X-RAY DIFFRACTION

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

NikR nickel-responsive regulator

Helicobacter pylori

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 SULFATE ION × 2	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 4	NICKEL (II) ION × 4 SULFATE ION × 3	Consistent with protein count
3	Protein homooligomer	Homooligomer	Protein 4	NICKEL (II) ION × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	NIKR_HELPY
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–88； UniProt 61–148 Author chain B； PDBConstruct 1–88； UniProt 61–148 Author chain C； PDBConstruct 1–88； UniProt 61–148 Author chain D； PDBConstruct 1–88； UniProt 61–148 Author chain E； PDBConstruct 1–88； UniProt 61–148 Author chain F； PDBConstruct 1–88； UniProt 61–148 Author chain G； PDBConstruct 1–88； UniProt 61–148 Author chain H； PDBConstruct 1–88； UniProt 61–148 Author chain I； PDBConstruct 1–88； UniProt 61–148 Author chain J； PDBConstruct 1–88； UniProt 61–148

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	3qsi
Deposition date deposition_date	2011-02-21
Structure title title	Nickel binding domain of NikR from Helicobacter pylori disclosing partial metal occupancy
Keywords keywords	NIKR, nickel, Helicobacter pylori, DNA-binding, transcription regulator, 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.

3qsi__assembly_2__model_1

Assembly 2 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

3qsi__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3qsi__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	19.91 Å
Rg (electron density)	18.61 Å
Total Rg	19.41 Å
Atom count	2445
Residues	317
Excluded volume	43551 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3qsi__assembly_1__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3qsi__assembly_2__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`3qsi__assembly_3__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	NikR nickel-responsive regulator
Molecular weight formula_weight	10128.5 kDa
Source method src_method	man
Copy count entity_count	10

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,C,D,A,F,G,H,E,J,I
Atom count atom_count	6138

DESKIAVLVVIYDHHQRELNQRMIDIQHASGTHVLCTTHIHMDEHNCLETIILQGNSFEIQRLQLEIGGLRGVKFAKLTKASSFEYNE

Source Source

Source organism organism	Helicobacter pylori
Common name common_name	Campylobacter pylori
NCBI taxonomy ID ncbi_taxonomy_id	210
Host organism host_organism	Escherichia coli

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	9

Entity 3 Entity 3 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	5

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6. Fold Classification (SCOP + CATH) 20 domains

SCOP 2.08 (10 domains)

Domain ID domain_id	d3qsia_
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.58.18.0 — automated matches

Domain ID domain_id	d3qsib_
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.58.18.0 — automated matches

Domain ID domain_id	d3qsic_
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.58.18.0 — automated matches

Domain ID domain_id	d3qsid_
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.58.18.0 — automated matches

Domain ID domain_id	d3qsie_
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.58.18.0 — automated matches

Domain ID domain_id	d3qsif_
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.58.18.0 — automated matches

Domain ID domain_id	d3qsig_
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.58.18.0 — automated matches

Domain ID domain_id	d3qsih_
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.58.18.0 — automated matches

Domain ID domain_id	d3qsii_
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.58.18.0 — automated matches

Domain ID domain_id	d3qsij_
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.58.18.0 — automated matches

CATH v4.4 (10 domains)

Domain ID domain_id	3qsiA00
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	3qsiB00
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	3qsiC00
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	3qsiD00
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	3qsiE00
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	3qsiF00
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	3qsiG00
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	3qsiH00
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	3qsiI00
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	3qsiJ00
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	147.379 Å
Unit-cell length b length_b	79.400 Å
Unit-cell length c length_c	122.423 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	122.28 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	40

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

Resolution resolution	3.080 Å
Low-resolution limit resolution_low	103.500 Å
R factor r_factor	0.2620
R_work r_work	0.2573
R_free r_free	0.3036

Nickel binding domain of NikR from Helicobacter pylori disclosing partial metal occupancy

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

NikR 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

3qsi__assembly_2__model_1

3qsi__assembly_2__model_1 | I(q)

3qsi__assembly_2__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 non-polymer

6. Fold Classification (SCOP + CATH) 20 domains

SCOP 2.08 (10 domains)

CATH v4.4 (10 domains)

7. Citations (1)

Nickel binding domain of NikR from Helicobacter pylori disclosing partial metal occupancy

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

NikR 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

3qsi__assembly_2__model_1

3qsi__assembly_2__model_1 | I(q)

3qsi__assembly_2__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 non-polymer

6. Fold Classification (SCOP + CATH) 20 domains

SCOP 2.08 (10 domains)

CATH v4.4 (10 domains)

7. Citations (1)