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3foo

A Triangular Cytochrome b562 Superstructure Mediated by Ni Coordination - Monoclinic Form

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

Soluble cytochrome b562

Escherichia coli

UniProt P0ABE7

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein homooligomer Homooligomer Protein 3 PROTOPORPHYRIN IX CONTAINING FE × 3 N-1,10-phenanthrolin-5-ylacetamide × 3 NICKEL (II) ION × 6 water × 3 Consistent with protein count
2 Protein homooligomer Homooligomer Protein 3 PROTOPORPHYRIN IX CONTAINING FE × 3 N-1,10-phenanthrolin-5-ylacetamide × 3 NICKEL (II) ION × 6 water × 3 Consistent with protein count
3 Protein homooligomer Homooligomer Protein 3 PROTOPORPHYRIN IX CONTAINING FE × 3 N-1,10-phenanthrolin-5-ylacetamide × 3 NICKEL (II) ION × 6 water × 3 Consistent with protein count
4 Protein homooligomer Homooligomer Protein 3 PROTOPORPHYRIN IX CONTAINING FE × 3 N-1,10-phenanthrolin-5-ylacetamide × 3 NICKEL (II) ION × 6 water × 3 Consistent with protein count

Other States of the Same Protein in the Database

Monomer
1apc 1m6t 1qpu 1qq3 256b 256b 2bc5 2bc5 2bc5 2bc5 3fop 3fop

78 assemblies; showing the first 12

Homodimer
1lm3 2bc5 2bc5 3de8 3de8 3hnk 3hnl 3l1m 3tol 3tol 3tom 3tom

35 assemblies; showing the first 12

Homotetramer
2bc5 2bc5 2bc5 2bc5 2qla 3c62 3c63 3de8 3hni 3hni 3hnj 3hnl

36 assemblies; showing the first 12

Other homooligomers
3de9 3foo 3foo 3foo 3foo 3fop 3m15 3m4b 6dhz 6ot4 6ot7 6ot8

39 assemblies; showing the first 12

Heteromeric or nucleic-acid complex
10kt 11td 11tf 11th 11tk 11tl 22em 24xy 24xz 25ik 25il 28vj

635 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name C562_ECOLX
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–106； UniProt 23–128 Author chain B； PDBConstruct 1–106； UniProt 23–128 Author chain C； PDBConstruct 1–106； UniProt 23–128 Author chain D； PDBConstruct 1–106； UniProt 23–128 Author chain E； PDBConstruct 1–106； UniProt 23–128 Author chain F； PDBConstruct 1–106； UniProt 23–128 Author chain G； PDBConstruct 1–106； UniProt 23–128 Author chain H； PDBConstruct 1–106； UniProt 23–128 Author chain I； PDBConstruct 1–106； UniProt 23–128 Author chain J； PDBConstruct 1–106； UniProt 23–128 Author chain K； PDBConstruct 1–106； UniProt 23–128 Author chain L； PDBConstruct 1–106； UniProt 23–128

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_id3foo
Deposition date deposition_date2008-12-30
Structure title titleA Triangular Cytochrome b562 Superstructure Mediated by Ni Coordination - Monoclinic Form
Keywords keywordsFour Helix Bundle, Electron transport, Heme, Iron, Metal-binding, Transport; ELECTRON 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.

3foo__assembly_1__model_1

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

Download this curve (.dat)

3foo__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.

3foo__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）24.74 Å
Rg (electron density)23.79 Å
Total Rg24.60 Å
Atom count2601
Residues318
Excluded volume45999 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 3foo__assembly_1__model_1 trimeric （3） Success 4.1.3-1-20251215 (887e7ef) View Download
2 1 3foo__assembly_2__model_1 trimeric （3） Success 4.1.3-1-20251215 (887e7ef) View Download
3 1 3foo__assembly_3__model_1 trimeric （3） Success 4.1.3-1-20251215 (887e7ef) View Download
4 1 3foo__assembly_4__model_1 trimeric （3） 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) 24 domains

SCOP 2.08 (12 domains)

Domain ID domain_idd3fooa_
Class classa — All alpha proteins
Fold Fold folda.24 — Four-helical up-and-down bundle
Superfamily Superfamily superfamilya.24.3 — Cytochromes
Family Family familya.24.3.1 — Cytochrome b562
Domain ID domain_idd3foob_
Class classa — All alpha proteins
Fold Fold folda.24 — Four-helical up-and-down bundle
Superfamily Superfamily superfamilya.24.3 — Cytochromes
Family Family familya.24.3.1 — Cytochrome b562
Domain ID domain_idd3fooc_
Class classa — All alpha proteins
Fold Fold folda.24 — Four-helical up-and-down bundle
Superfamily Superfamily superfamilya.24.3 — Cytochromes
Family Family familya.24.3.1 — Cytochrome b562
Domain ID domain_idd3food_
Class classa — All alpha proteins
Fold Fold folda.24 — Four-helical up-and-down bundle
Superfamily Superfamily superfamilya.24.3 — Cytochromes
Family Family familya.24.3.1 — Cytochrome b562
Domain ID domain_idd3fooe_
Class classa — All alpha proteins
Fold Fold folda.24 — Four-helical up-and-down bundle
Superfamily Superfamily superfamilya.24.3 — Cytochromes
Family Family familya.24.3.1 — Cytochrome b562
Domain ID domain_idd3foof_
Class classa — All alpha proteins
Fold Fold folda.24 — Four-helical up-and-down bundle
Superfamily Superfamily superfamilya.24.3 — Cytochromes
Family Family familya.24.3.1 — Cytochrome b562
Domain ID domain_idd3foog_
Class classa — All alpha proteins
Fold Fold folda.24 — Four-helical up-and-down bundle
Superfamily Superfamily superfamilya.24.3 — Cytochromes
Family Family familya.24.3.1 — Cytochrome b562
Domain ID domain_idd3fooh_
Class classa — All alpha proteins
Fold Fold folda.24 — Four-helical up-and-down bundle
Superfamily Superfamily superfamilya.24.3 — Cytochromes
Family Family familya.24.3.1 — Cytochrome b562
Domain ID domain_idd3fooi_
Class classa — All alpha proteins
Fold Fold folda.24 — Four-helical up-and-down bundle
Superfamily Superfamily superfamilya.24.3 — Cytochromes
Family Family familya.24.3.1 — Cytochrome b562
Domain ID domain_idd3fooj_
Class classa — All alpha proteins
Fold Fold folda.24 — Four-helical up-and-down bundle
Superfamily Superfamily superfamilya.24.3 — Cytochromes
Family Family familya.24.3.1 — Cytochrome b562
Domain ID domain_idd3fook_
Class classa — All alpha proteins
Fold Fold folda.24 — Four-helical up-and-down bundle
Superfamily Superfamily superfamilya.24.3 — Cytochromes
Family Family familya.24.3.1 — Cytochrome b562
Domain ID domain_idd3fool_
Class classa — All alpha proteins
Fold Fold folda.24 — Four-helical up-and-down bundle
Superfamily Superfamily superfamilya.24.3 — Cytochromes
Family Family familya.24.3.1 — Cytochrome b562

CATH v4.4 (12 domains)

Domain ID domain_id3fooA00
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
Homologous superfamily homologous superfamily10 — Cytochrome c/b562
Domain ID domain_id3fooB00
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
Homologous superfamily homologous superfamily10 — Cytochrome c/b562
Domain ID domain_id3fooC00
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
Homologous superfamily homologous superfamily10 — Cytochrome c/b562
Domain ID domain_id3fooD00
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
Homologous superfamily homologous superfamily10 — Cytochrome c/b562
Domain ID domain_id3fooE00
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
Homologous superfamily homologous superfamily10 — Cytochrome c/b562
Domain ID domain_id3fooF00
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
Homologous superfamily homologous superfamily10 — Cytochrome c/b562
Domain ID domain_id3fooG00
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
Homologous superfamily homologous superfamily10 — Cytochrome c/b562
Domain ID domain_id3fooH00
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
Homologous superfamily homologous superfamily10 — Cytochrome c/b562
Domain ID domain_id3fooI00
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
Homologous superfamily homologous superfamily10 — Cytochrome c/b562
Domain ID domain_id3fooJ00
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
Homologous superfamily homologous superfamily10 — Cytochrome c/b562
Domain ID domain_id3fooK00
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
Homologous superfamily homologous superfamily10 — Cytochrome c/b562
Domain ID domain_id3fooL00
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
Homologous superfamily homologous superfamily10 — Cytochrome c/b562
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7. Citations (1)