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Crystal structure of particulate methane monooxygenase from Methylococcus capsulatus (Bath)

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

Methane monooxygenase subunit B2

OrganismNot specified

UniProt Q49104

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 9 Methane monooxygenase subunit A2 × 3 （Q607G3） Methane monooxygenase subunit C2 × 3 （O05111） COPPER (II) ION × 3 ZINC ION × 9 DINUCLEAR COPPER ION × 3 water × 3 Consistent with protein count

Other States of the Same Protein in the Database

Monomer

None

Homodimer

None

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
1yew 1yew 1yew 1yew 1yew 1yew 3rgb

7 assemblies

View Construct and Data Evidence
UniProt name Q49104_METCA
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–414； UniProt 1–414 Author chain E； PDBConstruct 1–414； UniProt 1–414 Author chain I； PDBConstruct 1–414； UniProt 1–414

Methane monooxygenase subunit A2

OrganismNot specified

UniProt Q607G3

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 9 Methane monooxygenase subunit B2 × 3 （Q49104） Methane monooxygenase subunit C2 × 3 （O05111） COPPER (II) ION × 3 ZINC ION × 9 DINUCLEAR COPPER ION × 3 water × 3 Consistent with protein count

Other States of the Same Protein in the Database

Monomer

None

Homodimer

None

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
1yew 1yew 1yew 1yew 1yew 1yew 3rgb 7ev9 7s4h 7s4i 7s4j 7s4k

25 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name Q607G3_METCA
Isoform —
PDB entities 2
Chains and sequence ranges Author chain B； PDBConstruct 1–247； UniProt 1–247 Author chain F； PDBConstruct 1–247； UniProt 1–247 Author chain J； PDBConstruct 1–247； UniProt 1–247

Methane monooxygenase subunit C2

OrganismNot specified

UniProt O05111

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 9 Methane monooxygenase subunit B2 × 3 （Q49104） Methane monooxygenase subunit A2 × 3 （Q607G3） COPPER (II) ION × 3 ZINC ION × 9 DINUCLEAR COPPER ION × 3 water × 3 Consistent with protein count

Other States of the Same Protein in the Database

Monomer

None

Homodimer

None

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
1yew 1yew 1yew 1yew 1yew 1yew 3rgb 7yzy

8 assemblies

View Construct and Data Evidence
UniProt name O05111_METCA
Isoform —
PDB entities 3
Chains and sequence ranges Author chain C； PDBConstruct 1–289； UniProt 1–289 Author chain G； PDBConstruct 1–289； UniProt 1–289 Author chain K； PDBConstruct 1–289； UniProt 1–289

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_id3rgb
Deposition date deposition_date2011-04-08
Structure title titleCrystal structure of particulate methane monooxygenase from Methylococcus capsulatus (Bath)
Keywords keywordsmembrane, OXIDOREDUCTASE; OXIDOREDUCTASE
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.

3rgb__assembly_1__model_1

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

Download this curve (.dat)

3rgb__assembly_1__model_1 | I(q)

10-2 10-1 106 107 108 q (1/Angstrom) I(q)
100 plotted points; both axes use logarithmic scales.

3rgb__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）42.04 Å
Rg (electron density)40.95 Å
Total Rg41.56 Å
Atom count19734
Residues2439
Excluded volume355700 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 3rgb__assembly_1__model_1 nonameric （9） 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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6. Fold Classification (SCOP + CATH) 15 domains

CATH v4.4 (15 domains)

Domain ID domain_id3rgbA01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology120 — Jelly Rolls
Homologous superfamily homologous superfamily570 — Particulate methane monooxygenase, b subunit. Chain: A, domain 1
Domain ID domain_id3rgbA02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology287 — Helix Hairpins
Homologous superfamily homologous superfamily710 — Helix hairpin bin
Domain ID domain_id3rgbA03
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily1580 — Particulate methane monooxygenase, b subunit. Chain: A, domain 3
Domain ID domain_id3rgbB00
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology1450 — particulate methane monooxygenase, chain B
Homologous superfamily homologous superfamily10 — Ammonia/particulate methane monooxygenase, subunit A
Domain ID domain_id3rgbC00
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology1050 — Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2
Homologous superfamily homologous superfamily50 — Particulate methane monooxygenase subunit c2. Chain: C
Domain ID domain_id3rgbE01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology120 — Jelly Rolls
Homologous superfamily homologous superfamily570 — Particulate methane monooxygenase, b subunit. Chain: A, domain 1
Domain ID domain_id3rgbE02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology287 — Helix Hairpins
Homologous superfamily homologous superfamily710 — Helix hairpin bin
Domain ID domain_id3rgbE03
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily1580 — Particulate methane monooxygenase, b subunit. Chain: A, domain 3
Domain ID domain_id3rgbF00
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology1450 — particulate methane monooxygenase, chain B
Homologous superfamily homologous superfamily10 — Ammonia/particulate methane monooxygenase, subunit A
Domain ID domain_id3rgbG00
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology1050 — Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2
Homologous superfamily homologous superfamily50 — Particulate methane monooxygenase subunit c2. Chain: C
Domain ID domain_id3rgbI01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology120 — Jelly Rolls
Homologous superfamily homologous superfamily570 — Particulate methane monooxygenase, b subunit. Chain: A, domain 1
Domain ID domain_id3rgbI02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology287 — Helix Hairpins
Homologous superfamily homologous superfamily710 — Helix hairpin bin
Domain ID domain_id3rgbI03
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily1580 — Particulate methane monooxygenase, b subunit. Chain: A, domain 3
Domain ID domain_id3rgbJ00
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology1450 — particulate methane monooxygenase, chain B
Homologous superfamily homologous superfamily10 — Ammonia/particulate methane monooxygenase, subunit A
Domain ID domain_id3rgbK00
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology1050 — Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2
Homologous superfamily homologous superfamily50 — Particulate methane monooxygenase subunit c2. Chain: C
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7. Citations (1)