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6yd0

XFEL structure of the Soluble methane monooxygenase hydroxylase and regulatory subunit complex, from Methylosinus trichosporium OB3b, diferric state

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

Methane monooxygenase

OrganismNot specified

UniProt A0A2D2D5X7

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 8 Methane monooxygenase component A alpha chain × 2 （P27353） Methane monooxygenase × 2 （A0A1A6FHH2） Methane monooxygenase regulatory protein B × 2 （P27356） GLYCEROL × 2 FE (III) ION × 4 water × 8 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
6vk4 6vk5 6vk6 6vk7 6vk8 6yd0 6ydi 6ydu 7m8q 7m8r 7s6q 7s6r

15 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name A0A2D2D5X7_METTR
Isoform —
PDB entities 1
Chains and sequence ranges Author chain B； PDBConstruct 1–395； UniProt 1–395

Methane monooxygenase component A alpha chain

OrganismNot specified

UniProt P27353

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 8 Methane monooxygenase × 2 （A0A2D2D5X7） Methane monooxygenase × 2 （A0A1A6FHH2） Methane monooxygenase regulatory protein B × 2 （P27356） GLYCEROL × 2 FE (III) ION × 4 water × 8 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
1mhy 1mhz 6yd0 6ydi 6ydu 6yy3

6 assemblies

View Construct and Data Evidence
UniProt name MEMA_METTR
Isoform —
PDB entities 2
Chains and sequence ranges Author chain D； PDBConstruct 1–526； UniProt 1–526

Methane monooxygenase

OrganismNot specified

UniProt A0A1A6FHH2

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 8 Methane monooxygenase × 2 （A0A2D2D5X7） Methane monooxygenase component A alpha chain × 2 （P27353） Methane monooxygenase regulatory protein B × 2 （P27356） GLYCEROL × 2 FE (III) ION × 4 water × 8 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
6yd0 6ydi 6ydu 6yy3

4 assemblies

View Construct and Data Evidence
UniProt name A0A1A6FHH2_9RHIZ
Isoform —
PDB entities 3
Chains and sequence ranges Author chain F； PDBConstruct 1–169； UniProt 1–169

Methane monooxygenase regulatory protein B

Methylosinus trichosporium OB3b

UniProt P27356

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 8 Methane monooxygenase × 2 （A0A2D2D5X7） Methane monooxygenase component A alpha chain × 2 （P27353） Methane monooxygenase × 2 （A0A1A6FHH2） GLYCEROL × 2 FE (III) ION × 4 water × 8 Consistent with protein count

Other States of the Same Protein in the Database

Monomer
2mob

1 assemblies

Homodimer

None

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
6yd0 6ydi 6ydu 6yy3

4 assemblies

View Construct and Data Evidence
UniProt name MMOB_METTR
Isoform —
PDB entities 4
Chains and sequence ranges Author chain G； PDBConstruct 1–138； UniProt 1–138

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_id6yd0
Deposition date deposition_date2020-03-19
Structure title titleXFEL structure of the Soluble methane monooxygenase hydroxylase and regulatory subunit complex, from Methylosinus trichosporium OB3b, diferric state
Keywords keywordsFerritin superfamily, Soluble methane monooxygenase, Di-iron oxygen activation, Substrate oxidation., 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.

6yd0__assembly_1__model_1

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

Download this curve (.dat)

6yd0__assembly_1__model_1 | I(q)

10-2 10-1 106 107 108 109 q (1/Angstrom) I(q)
100 plotted points; both axes use logarithmic scales.

6yd0__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）40.67 Å
Rg (electron density)40.37 Å
Total Rg40.72 Å
Atom count19490
Residues2418
Excluded volume344770 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 6yd0__assembly_1__model_1 octameric （8） 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) 4 domains

SCOP 2.08 (4 domains)

Domain ID domain_idd6yd0b_
Class classa — All alpha proteins
Fold Fold folda.25 — Ferritin-like
Superfamily Superfamily superfamilya.25.1 — Ferritin-like
Family Family familya.25.1.2 — Ribonucleotide reductase-like
Domain ID domain_idd6yd0d_
Class classa — All alpha proteins
Fold Fold folda.25 — Ferritin-like
Superfamily Superfamily superfamilya.25.1 — Ferritin-like
Family Family familya.25.1.2 — Ribonucleotide reductase-like
Domain ID domain_idd6yd0f_
Class classa — All alpha proteins
Fold Fold folda.23 — Open three-helical up-and-down bundle
Superfamily Superfamily superfamilya.23.3 — Methane monooxygenase hydrolase, gamma subunit
Family Family familya.23.3.1 — Methane monooxygenase hydrolase, gamma subunit
Domain ID domain_idd6yd0g_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.137 — Monooxygenase (hydroxylase) regulatory protein
Superfamily Superfamily superfamilyd.137.1 — Monooxygenase (hydroxylase) regulatory protein
Family Family familyd.137.1.1 — Monooxygenase (hydroxylase) regulatory protein
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7. Citations (1)