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3dp8

Structural characterization of a putative endogenous metal chelator in the periplasmic nickel transporter NikA (nickel butane-1,2,4-tricarboxylate form)

Method: X-RAY DIFFRACTION
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Nickel-binding periplasmic protein

Escherichia coli

UniProt P33590

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein monomer Monomer Protein 1 NICKEL (II) ION × 1 ACETATE ION × 4 SULFATE ION × 1 CHLORIDE ION × 2 (2R)-butane-1,2,4-tricarboxylic acid × 1 GLYCEROL × 4 water × 1 Consistent with protein count
2 Protein monomer Monomer Protein 1 NICKEL (II) ION × 1 ACETATE ION × 4 CHLORIDE ION × 3 (2R)-butane-1,2,4-tricarboxylic acid × 1 GLYCEROL × 4 water × 1 Consistent with protein count
3 Protein monomer Monomer Protein 1 NICKEL (II) ION × 1 ACETATE ION × 3 CHLORIDE ION × 2 (2R)-butane-1,2,4-tricarboxylic acid × 1 water × 1 Consistent with protein count

Other States of the Same Protein in the Database

Monomer
1uiu 1uiu 1uiv 1uiv 1zlq 1zlq 2noo 3dp8 3dp8 3dp8 3e3k 3e3k

60 assemblies; showing the first 12

Homodimer
9t0v

1 assemblies

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex

None

View Construct and Data Evidence
UniProt name NIKA_ECOLI
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–502； UniProt 23–524 Author chain B； PDBConstruct 1–502； UniProt 23–524 Author chain C； PDBConstruct 1–502； UniProt 23–524

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_id3dp8
Deposition date deposition_date2008-07-07
Structure title titleStructural characterization of a putative endogenous metal chelator in the periplasmic nickel transporter NikA (nickel butane-1,2,4-tricarboxylate form)
Keywords keywordsNickel, Nickellophore, Butane-1, 2, 4-tricarboxylate, Transport, METAL TRANSPORT; METAL TRANSPORT
Experimental Method methodX-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.

3dp8__assembly_2__model_1

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

Download this curve (.dat)

3dp8__assembly_2__model_1 | I(q)

10-2 10-1 105 106 107 q (1/Angstrom) I(q)
100 plotted points; both axes use logarithmic scales.

3dp8__assembly_2__model_1 | P(r) · Pending

The new assembly/model P(r) has not been calculated yet This placeholder does not display legacy data r (Angstrom) P(r)
P(r) will be calculated and displayed separately for the same assembly/model.
Rg（Guinier）24.67 Å
Rg (electron density)23.61 Å
Total Rg24.51 Å
Atom count4004
Residues497
Excluded volume71414 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 3dp8__assembly_1__model_1 monomeric （1） Success 4.1.3-1-20251215 (887e7ef) View Download
2 1 3dp8__assembly_2__model_1 monomeric （1） Success 4.1.3-1-20251215 (887e7ef) View Download
3 1 3dp8__assembly_3__model_1 monomeric （1） 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 (8)

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6. Fold Classification (SCOP + CATH) 9 domains

SCOP 2.08 (3 domains)

Domain ID domain_idd3dp8a_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.94 — Periplasmic binding protein-like II
Superfamily Superfamily superfamilyc.94.1 — Periplasmic binding protein-like II
Family Family familyc.94.1.1 — Phosphate binding protein-like
Domain ID domain_idd3dp8b_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.94 — Periplasmic binding protein-like II
Superfamily Superfamily superfamilyc.94.1 — Periplasmic binding protein-like II
Family Family familyc.94.1.1 — Phosphate binding protein-like
Domain ID domain_idd3dp8c_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.94 — Periplasmic binding protein-like II
Superfamily Superfamily superfamilyc.94.1 — Periplasmic binding protein-like II
Family Family familyc.94.1.1 — Phosphate binding protein-like

CATH v4.4 (6 domains)

Domain ID domain_id3dp8A01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology190 — D-Maltodextrin-Binding Protein; domain 2
Homologous superfamily homologous superfamily10 — Periplasmic binding protein-like II
Domain ID domain_id3dp8A02
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology105 — Dipeptide-binding Protein; domain 3
Homologous superfamily homologous superfamily10 — Dipeptide-binding Protein; Domain 3
Domain ID domain_id3dp8B01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology190 — D-Maltodextrin-Binding Protein; domain 2
Homologous superfamily homologous superfamily10 — Periplasmic binding protein-like II
Domain ID domain_id3dp8B02
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology105 — Dipeptide-binding Protein; domain 3
Homologous superfamily homologous superfamily10 — Dipeptide-binding Protein; Domain 3
Domain ID domain_id3dp8C01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology190 — D-Maltodextrin-Binding Protein; domain 2
Homologous superfamily homologous superfamily10 — Periplasmic binding protein-like II
Domain ID domain_id3dp8C02
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology105 — Dipeptide-binding Protein; domain 3
Homologous superfamily homologous superfamily10 — Dipeptide-binding Protein; Domain 3
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7. Citations (1)