← Back to search
1yew

Crystal structure of particulate methane monooxygenase

Method: X-RAY DIFFRACTION
▼

1. Protein Identity and Related Structures Protein Identity & Related Structures

particulate methane monooxygenase, B subunit

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 3 particulate methane monooxygenase, A subunit × 1 （Q607G3） particulate methane monooxygenase subunit C2 × 1 （O05111） COPPER (II) ION × 1 ZINC ION × 3 DINUCLEAR COPPER ION × 1 Consistent with protein count
2 Protein heterocomplex Heteromer Protein 3 particulate methane monooxygenase, A subunit × 1 （Q607G3） particulate methane monooxygenase subunit C2 × 1 （O05111） COPPER (II) ION × 1 ZINC ION × 4 DINUCLEAR COPPER ION × 1 Consistent with protein count
3 Protein heterocomplex Heteromer Protein 3 particulate methane monooxygenase, A subunit × 1 （Q607G3） particulate methane monooxygenase subunit C2 × 1 （O05111） COPPER (II) ION × 1 ZINC ION × 1 DINUCLEAR COPPER ION × 1 Consistent with protein count
4 Protein heterocomplex Heteromer Protein 18 particulate methane monooxygenase, A subunit × 6 （Q607G3） particulate methane monooxygenase subunit C2 × 6 （O05111） COPPER (II) ION × 6 ZINC ION × 16 DINUCLEAR COPPER ION × 6 Consistent with protein count
5 Protein heterocomplex Heteromer Protein 18 particulate methane monooxygenase, A subunit × 6 （Q607G3） particulate methane monooxygenase subunit C2 × 6 （O05111） COPPER (II) ION × 6 ZINC ION × 16 DINUCLEAR COPPER ION × 6 Consistent with protein count
6 Protein heterocomplex Heteromer Protein 9 particulate methane monooxygenase, A subunit × 3 （Q607G3） particulate methane monooxygenase subunit C2 × 3 （O05111） COPPER (II) ION × 3 ZINC ION × 8 DINUCLEAR COPPER ION × 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 1–382； UniProt 33–414 Author chain E； PDBConstruct 1–382； UniProt 33–414 Author chain I； PDBConstruct 1–382； UniProt 33–414

particulate methane monooxygenase, A subunit

Methylococcus capsulatus

UniProt Q607G3

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 3 particulate methane monooxygenase, B subunit × 1 （Q49104） particulate methane monooxygenase subunit C2 × 1 （O05111） COPPER (II) ION × 1 ZINC ION × 3 DINUCLEAR COPPER ION × 1 Consistent with protein count
2 Protein heterocomplex Heteromer Protein 3 particulate methane monooxygenase, B subunit × 1 （Q49104） particulate methane monooxygenase subunit C2 × 1 （O05111） COPPER (II) ION × 1 ZINC ION × 4 DINUCLEAR COPPER ION × 1 Consistent with protein count
3 Protein heterocomplex Heteromer Protein 3 particulate methane monooxygenase, B subunit × 1 （Q49104） particulate methane monooxygenase subunit C2 × 1 （O05111） COPPER (II) ION × 1 ZINC ION × 1 DINUCLEAR COPPER ION × 1 Consistent with protein count
4 Protein heterocomplex Heteromer Protein 18 particulate methane monooxygenase, B subunit × 6 （Q49104） particulate methane monooxygenase subunit C2 × 6 （O05111） COPPER (II) ION × 6 ZINC ION × 16 DINUCLEAR COPPER ION × 6 Consistent with protein count
5 Protein heterocomplex Heteromer Protein 18 particulate methane monooxygenase, B subunit × 6 （Q49104） particulate methane monooxygenase subunit C2 × 6 （O05111） COPPER (II) ION × 6 ZINC ION × 16 DINUCLEAR COPPER ION × 6 Consistent with protein count
6 Protein heterocomplex Heteromer Protein 9 particulate methane monooxygenase, B subunit × 3 （Q49104） particulate methane monooxygenase subunit C2 × 3 （O05111） COPPER (II) ION × 3 ZINC ION × 8 DINUCLEAR COPPER ION × 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

particulate methane monooxygenase subunit C2

Methylococcus capsulatus

UniProt O05111

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 3 particulate methane monooxygenase, B subunit × 1 （Q49104） particulate methane monooxygenase, A subunit × 1 （Q607G3） COPPER (II) ION × 1 ZINC ION × 3 DINUCLEAR COPPER ION × 1 Consistent with protein count
2 Protein heterocomplex Heteromer Protein 3 particulate methane monooxygenase, B subunit × 1 （Q49104） particulate methane monooxygenase, A subunit × 1 （Q607G3） COPPER (II) ION × 1 ZINC ION × 4 DINUCLEAR COPPER ION × 1 Consistent with protein count
3 Protein heterocomplex Heteromer Protein 3 particulate methane monooxygenase, B subunit × 1 （Q49104） particulate methane monooxygenase, A subunit × 1 （Q607G3） COPPER (II) ION × 1 ZINC ION × 1 DINUCLEAR COPPER ION × 1 Consistent with protein count
4 Protein heterocomplex Heteromer Protein 18 particulate methane monooxygenase, B subunit × 6 （Q49104） particulate methane monooxygenase, A subunit × 6 （Q607G3） COPPER (II) ION × 6 ZINC ION × 16 DINUCLEAR COPPER ION × 6 Consistent with protein count
5 Protein heterocomplex Heteromer Protein 18 particulate methane monooxygenase, B subunit × 6 （Q49104） particulate methane monooxygenase, A subunit × 6 （Q607G3） COPPER (II) ION × 6 ZINC ION × 16 DINUCLEAR COPPER ION × 6 Consistent with protein count
6 Protein heterocomplex Heteromer Protein 9 particulate methane monooxygenase, B subunit × 3 （Q49104） particulate methane monooxygenase, A subunit × 3 （Q607G3） COPPER (II) ION × 3 ZINC ION × 8 DINUCLEAR COPPER ION × 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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id1yew
Deposition date deposition_date2004-12-28
Structure title titleCrystal structure of particulate methane monooxygenase
Keywords keywordsmembrane protein, methane, beta barrel, OXIDOREDUCTASE; OXIDOREDUCTASE, MEMBRANE PROTEIN
Experimental Method methodX-RAY DIFFRACTION
▼

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.

1yew__assembly_1__model_1

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

Download this curve (.dat)

1yew__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.

1yew__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）32.11 Å
Rg (electron density)31.62 Å
Total Rg32.34 Å
Atom count6591
Residues808
Excluded volume118720 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 1yew__assembly_1__model_1 trimeric （3） Success 4.1.3-1-20251215 (887e7ef) View Download
2 1 1yew__assembly_2__model_1 trimeric （3） Success 4.1.3-1-20251215 (887e7ef) View Download
3 1 1yew__assembly_3__model_1 trimeric （3） Success 4.1.3-1-20251215 (887e7ef) View Download
4 1 1yew__assembly_4__model_1 octadecameric （18） Success 4.1.3-1-20251215 (887e7ef) View Download
5 1 1yew__assembly_5__model_1 octadecameric （18） Success 4.1.3-1-20251215 (887e7ef) View Download
6 1 1yew__assembly_6__model_1 nonameric （9） Success 4.1.3-1-20251215 (887e7ef) View Download
▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (6)

▼

6. Fold Classification (SCOP + CATH) 15 domains

CATH v4.4 (15 domains)

Domain ID domain_id1yewA01
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_id1yewA02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology287 — Helix Hairpins
Homologous superfamily homologous superfamily710 — Helix hairpin bin
Domain ID domain_id1yewA03
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_id1yewB00
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_id1yewC00
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_id1yewE01
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_id1yewE02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology287 — Helix Hairpins
Homologous superfamily homologous superfamily710 — Helix hairpin bin
Domain ID domain_id1yewE03
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_id1yewF00
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_id1yewG00
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_id1yewI01
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_id1yewI02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology287 — Helix Hairpins
Homologous superfamily homologous superfamily710 — Helix hairpin bin
Domain ID domain_id1yewI03
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_id1yewJ00
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_id1yewK00
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
▶

7. Citations (1)