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9ovf

Rubredoxin covalently linked to benzo-18-crown-6

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

Rubredoxin-1

Desulfovibrio desulfuricans ATCC 27774

UniProt P04170

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein monomer Monomer Protein 1 FE (III) ION × 1 2,3,5,6,8,9,11,12,14,15-decahydro-1,4,7,10,13,16-benzohexaoxacyclooctadecine-18-thiol × 1 ACETATE ION × 2 SODIUM ION × 5 water × 1 Consistent with protein count
10 Protein monomer Monomer Protein 1 FE (III) ION × 1 2,3,5,6,8,9,11,12,14,15-decahydro-1,4,7,10,13,16-benzohexaoxacyclooctadecine-18-thiol × 1 ACETATE ION × 2 SODIUM ION × 2 water × 1 Consistent with protein count
2 Protein monomer Monomer Protein 1 FE (III) ION × 1 2,3,5,6,8,9,11,12,14,15-decahydro-1,4,7,10,13,16-benzohexaoxacyclooctadecine-18-thiol × 1 ACETATE ION × 1 SODIUM ION × 3 POLYETHYLENE GLYCOL (N=34) × 1 water × 1 Consistent with protein count
3 Protein monomer Monomer Protein 1 FE (III) ION × 1 2,3,5,6,8,9,11,12,14,15-decahydro-1,4,7,10,13,16-benzohexaoxacyclooctadecine-18-thiol × 1 ACETATE ION × 2 SODIUM ION × 4 water × 1 Consistent with protein count
4 Protein monomer Monomer Protein 1 FE (III) ION × 1 2,3,5,6,8,9,11,12,14,15-decahydro-1,4,7,10,13,16-benzohexaoxacyclooctadecine-18-thiol × 1 ACETATE ION × 2 SODIUM ION × 4 water × 1 Consistent with protein count
5 Protein monomer Monomer Protein 1 FE (III) ION × 1 2,3,5,6,8,9,11,12,14,15-decahydro-1,4,7,10,13,16-benzohexaoxacyclooctadecine-18-thiol × 1 ACETATE ION × 2 SODIUM ION × 4 POLYETHYLENE GLYCOL (N=34) × 1 water × 1 Consistent with protein count
6 Protein monomer Monomer Protein 1 FE (III) ION × 1 2,3,5,6,8,9,11,12,14,15-decahydro-1,4,7,10,13,16-benzohexaoxacyclooctadecine-18-thiol × 1 ACETATE ION × 2 SODIUM ION × 5 water × 1 Consistent with protein count
7 Protein monomer Monomer Protein 1 FE (III) ION × 1 2,3,5,6,8,9,11,12,14,15-decahydro-1,4,7,10,13,16-benzohexaoxacyclooctadecine-18-thiol × 1 ACETATE ION × 2 SODIUM ION × 4 water × 1 Consistent with protein count
8 Protein monomer Monomer Protein 1 FE (III) ION × 1 2,3,5,6,8,9,11,12,14,15-decahydro-1,4,7,10,13,16-benzohexaoxacyclooctadecine-18-thiol × 1 ACETATE ION × 1 SODIUM ION × 3 water × 1 Consistent with protein count
9 Protein monomer Monomer Protein 1 FE (III) ION × 1 2,3,5,6,8,9,11,12,14,15-decahydro-1,4,7,10,13,16-benzohexaoxacyclooctadecine-18-thiol × 1 ACETATE ION × 2 SODIUM ION × 5 water × 1 Consistent with protein count

Other States of the Same Protein in the Database

Monomer
6rxn 9ovf 9ovf 9ovf 9ovf 9ovf 9ovf 9ovf 9ovf 9ovf 9ovf

11 assemblies

Homodimer

None

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex

None

View Construct and Data Evidence
UniProt name RUBR1_DESDA
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–45； UniProt 1–45 Author chain B； PDBConstruct 1–45； UniProt 1–45 Author chain C； PDBConstruct 1–45； UniProt 1–45 Author chain D； PDBConstruct 1–45； UniProt 1–45 Author chain E； PDBConstruct 1–45； UniProt 1–45 Author chain F； PDBConstruct 1–45； UniProt 1–45 Author chain G； PDBConstruct 1–45； UniProt 1–45 Author chain H； PDBConstruct 1–45； UniProt 1–45 Author chain I； PDBConstruct 1–45； UniProt 1–45 Author chain J； PDBConstruct 1–45； UniProt 1–45

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_id9ovf
Deposition date deposition_date2025-05-29
Last revision last_revision2025-12-03
Structure title titleRubredoxin covalently linked to benzo-18-crown-6
Keywords keywordsbenzo-18-crown-6, Cys arylation, site-selective protein modification, 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.

9ovf__assembly_3__model_1

Assembly 3 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

9ovf__assembly_3__model_1 | I(q)

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

9ovf__assembly_3__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）11.45 Å
Rg (electron density)10.04 Å
Total Rg11.58 Å
Atom count385
Residues44
Excluded volume6907 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 9ovf__assembly_1__model_1 monomeric （1） Success 4.1.3-1-20251215 (887e7ef) View Download
2 1 9ovf__assembly_2__model_1 monomeric （1） Success 4.1.3-1-20251215 (887e7ef) View Download
3 1 9ovf__assembly_3__model_1 monomeric （1） Success 4.1.3-1-20251215 (887e7ef) View Download
4 1 9ovf__assembly_4__model_1 monomeric （1） Success 4.1.3-1-20251215 (887e7ef) View Download
5 1 9ovf__assembly_5__model_1 monomeric （1） Success 4.1.3-1-20251215 (887e7ef) View Download
6 1 9ovf__assembly_6__model_1 monomeric （1） Success 4.1.3-1-20251215 (887e7ef) View Download
7 1 9ovf__assembly_7__model_1 monomeric （1） Success 4.1.3-1-20251215 (887e7ef) View Download
8 1 9ovf__assembly_8__model_1 monomeric （1） Success 4.1.3-1-20251215 (887e7ef) View Download
9 1 9ovf__assembly_9__model_1 monomeric （1） Success 4.1.3-1-20251215 (887e7ef) View Download
10 1 9ovf__assembly_10__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 (7)

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7. Citations (1)