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1o7t

Metal nanoclusters bound to the Ferric Binding Protein from Neisseria gonorrhoeae.

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

IRON BINDING PROTEIN

NEISSERIA GONORRHOEAE

UniProt Q50964

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein monomer Monomer Protein 1 HF OXO CLUSTER HF5 × 1 water × 1 Consistent with protein count
2 Protein monomer Monomer Protein 1 HF OXO CLUSTER HF5 × 1 water × 1 Consistent with protein count
3 Protein monomer Monomer Protein 1 HF OXO CLUSTER HF5 × 1 water × 1 Consistent with protein count
4 Protein monomer Monomer Protein 1 SMALLEST HF-OXO-PHOSPHATE CLUSTER HF3 × 1 water × 1 Consistent with protein count
5 Protein monomer Monomer Protein 1 HF OXO CLUSTER HF5 × 1 water × 1 Consistent with protein count
6 Protein monomer Monomer Protein 1 HF OXO CLUSTER HF5 × 1 water × 1 Consistent with protein count
7 Protein monomer Monomer Protein 1 HF-OXO-PHOSPHATE CLUSTER PHF × 1 water × 1 Consistent with protein count
8 Protein monomer Monomer Protein 1 HF-OXO-PHOSPHATE CLUSTER PHF × 1 water × 1 Consistent with protein count
9 Protein monomer Monomer Protein 1 HF-OXO-PHOSPHATE CLUSTER PHF × 1 water × 1 Consistent with protein count

Other States of the Same Protein in the Database

Monomer
1d9y 1o7t 1o7t 1o7t 1o7t 1o7t 1o7t 1o7t 1o7t 1o7t 3tyh 3tyh

19 assemblies; showing the first 12

Homodimer

None

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex

None

View Construct and Data Evidence
UniProt name Q50964_NEIGO
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–309； UniProt 23–331 Author chain B； PDBConstruct 1–309； UniProt 23–331 Author chain C； PDBConstruct 1–309； UniProt 23–331 Author chain D； PDBConstruct 1–309； UniProt 23–331 Author chain E； PDBConstruct 1–309； UniProt 23–331 Author chain F； PDBConstruct 1–309； UniProt 23–331 Author chain G； PDBConstruct 1–309； UniProt 23–331 Author chain H； PDBConstruct 1–309； UniProt 23–331 Author chain I； PDBConstruct 1–309； UniProt 23–331

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_id1o7t
Deposition date deposition_date2002-11-12
Structure title titleMetal nanoclusters bound to the Ferric Binding Protein from Neisseria gonorrhoeae.
Keywords keywordsMETAL-BINDING PROTEIN, PERIPLASMIC FERRIC BINDING PROTEIN, HAFNIUM, METAL-OXO CLUSTER, METAL BINDING PROTEIN; METAL BINDING PROTEIN
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.

1o7t__assembly_1__model_1

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

Download this curve (.dat)

1o7t__assembly_1__model_1 | I(q)

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

1o7t__assembly_1__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）20.56 Å
Rg (electron density)20.01 Å
Total Rg20.51 Å
Atom count2403
Residues309
Excluded volume42918 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 1o7t__assembly_1__model_1 monomeric （1） Success 4.1.3-1-20251215 (887e7ef) View Download
2 1 1o7t__assembly_2__model_1 monomeric （1） Success 4.1.3-1-20251215 (887e7ef) View Download
3 1 1o7t__assembly_3__model_1 monomeric （1） Success 4.1.3-1-20251215 (887e7ef) View Download
4 1 1o7t__assembly_4__model_1 monomeric （1） Success 4.1.3-1-20251215 (887e7ef) View Download
5 1 1o7t__assembly_5__model_1 monomeric （1） Success 4.1.3-1-20251215 (887e7ef) View Download
6 1 1o7t__assembly_6__model_1 monomeric （1） Success 4.1.3-1-20251215 (887e7ef) View Download
7 1 1o7t__assembly_7__model_1 monomeric （1） Success 4.1.3-1-20251215 (887e7ef) View Download
8 1 1o7t__assembly_8__model_1 monomeric （1） Success 4.1.3-1-20251215 (887e7ef) View Download
9 1 1o7t__assembly_9__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 (5)

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6. Fold Classification (SCOP + CATH) 27 domains

SCOP 2.08 (9 domains)

Domain ID domain_idd1o7ta_
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_idd1o7tb_
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_idd1o7tc_
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_idd1o7td_
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_idd1o7te_
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_idd1o7tf_
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_idd1o7tg_
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_idd1o7th_
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_idd1o7ti_
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 (18 domains)

Domain ID domain_id1o7tA01
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_id1o7tA02
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_id1o7tB01
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_id1o7tB02
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_id1o7tC01
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_id1o7tC02
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_id1o7tD01
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_id1o7tD02
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_id1o7tE01
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_id1o7tE02
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_id1o7tF01
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_id1o7tF02
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_id1o7tG01
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_id1o7tG02
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_id1o7tH01
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_id1o7tH02
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_id1o7tI01
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_id1o7tI02
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
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7. Citations (1)