SAXSdb — 6ydi

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

Methane monooxygenase

OrganismNot specified

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 (II) ION × 4 water × 8	Consistent with protein count

Other States of the Same Protein in the Database

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 (II) ION × 4 water × 8	Consistent with protein count

Other States of the Same Protein in the Database

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 (II) ION × 4 water × 8	Consistent with protein count

Other States of the Same Protein in the Database

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 (II) ION × 4 water × 8	Consistent with protein count

Other States of the Same Protein in the Database

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_id	6ydi
Deposition date deposition_date	2020-03-20
Structure title title	XFEL structure of the Soluble methane monooxygenase hydroxylase and regulatory subunit complex, from Methylosinus trichosporium OB3b, diferrous state
Keywords keywords	Ferritin superfamily, Soluble methane monooxygenase, Di-iron oxygen activation, Substrate oxidation., OXIDOREDUCTASE; OXIDOREDUCTASE
Experimental Method method	X-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.

6ydi__assembly_1__model_1

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

Download this curve (.dat)

6ydi__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6ydi__assembly_1__model_1 | P(r) · Pending

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 Rg	40.72 Å
Atom count	19416
Residues	2408
Excluded volume	343410 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6ydi__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)

Entity 1 Entity 1 polymer

Description description	Methane monooxygenase
Molecular weight formula_weight	45295.3 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B
Atom count atom_count	10205

MSQPQSSQVTKRGLTDPERAAIIAAAVPDHALDTQRKYHYFIQPRWKRLSEYEQLSCYAQPNPDWIAGGLDWGDWTQKFHGGRPSWGNESTELRTTDWYRHRDPARRWHHPYVKDKSEEARYTQRFLAAYSSEGSIRTIDPYWRDEILNKYFGALLYSEYGLFNAHSSVGRDCLSDTIRQTAVFAALDKVDNAQMIQMERLFIAKLVPGFDASTDVPKKIWTTDPIYSGARATVQEIWQGVQDWNEILWAGHAVYDATFGQFARREFFQRLATVYGDTLTPFFTAQSQTYFQTTRGAIDDLFVYCLANDSEFGAHNRTFLNAWTEHYLASSVAALKDFVGLYAKVEKVAGATDRAGVSEALQRVFGDWKIDYADKIGFRVDVDQKVDAVLAGYKN

Entity 2 Entity 2 polymer

Description description	Methane monooxygenase component A alpha chain
Molecular weight formula_weight	60031.3 kDa
EC 编号 ec_number	1.14.13.25
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D

MAISLATKAATDALKVNRAPVGVEPQEVHKWLQSFNWDFKENRTKYPTKYHMANETKEQFKVIAKEYARMEAAKDERQFGTLLDGLTRLGAGNKVHPRWGETMKVISNFLEVGEYNAIAASAMLWDSATAAEQKNGYLAQVLDEIRHTHQCAFINHYYSKHYHDPAGHNDARRTRAIGPLWKGMKRVFADGFISGDAVECSVNLQLVGEACFTNPLIVAVTEWASANGDEITPTVFLSVETDELRHMANGYQTVVSIANDPASAKFLNTDLNNAFWTQQKYFTPVLGYLFEYGSKFKVEPWVKTWNRWVYEDWGGIWIGRLGKYGVESPASLRDAKRDAYWAHHDLALAAYAMWPLGFARLALPDEEDQAWFEANYPGWADHYGKIFNEWKKLGYEDPKSGFIPYQWLLANGHDVYIDRVSQVPFIPSLAKGTGSLRVHEFNGKKHSLTDDWGERQWLIEPERYECHNVFEQYEGRELSEVIAEGHGVRSDGKTLIAQPHTRGDNLWTLEDIKRAGCVFPDPLAKF

Entity 3 Entity 3 polymer

Description description	Methane monooxygenase
Molecular weight formula_weight	19444.4 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	F

MAKREPIHDNSIRTEWEAKIAKLTSVDQATKFIQDFRLAYTSPFRKSYDIDVDYQYIERKIEEKLSVLKTEKLPVADLITKATTGEDAAAVEATWIAKIKAAKSKYEAERIHIEFRQLYKPPVLPVNVFLRTDAALGTVLMEIRNTDYYGTPLEGLRKERGVKVLHLQA

Entity 4 Entity 4 polymer

Description description	Methane monooxygenase regulatory protein B
Molecular weight formula_weight	14896.9 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	G

MSSAHNAYNAGIMQKTGKAFADEFFAEENQVVHESNAVVLVLMKSDEIDAIIEDIVLKGGKAKNPSIVVEDKAGFWWIKADGAIEIDAAEAGELLGKPFSVYDLLINVSSTVGRAYTLGTKFTITSELMGLDRALTDI

Source Source

Source organism organism	Methylosinus trichosporium OB3b
NCBI taxonomy ID ncbi_taxonomy_id	595536
Host organism host_organism	Escherichia coli

Entity 5 Entity 5 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	nat
Copy count entity_count	1

Entity 6 Entity 6 non-polymer

Description description	FE (II) ION
Molecular weight formula_weight	55.8 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 7 Entity 7 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	469

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6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d6ydib_
Class class	a — All alpha proteins
Fold Fold fold	a.25 — Ferritin-like
Superfamily Superfamily superfamily	a.25.1 — Ferritin-like
Family Family family	a.25.1.2 — Ribonucleotide reductase-like

Domain ID domain_id	d6ydid_
Class class	a — All alpha proteins
Fold Fold fold	a.25 — Ferritin-like
Superfamily Superfamily superfamily	a.25.1 — Ferritin-like
Family Family family	a.25.1.2 — Ribonucleotide reductase-like

Domain ID domain_id	d6ydif_
Class class	a — All alpha proteins
Fold Fold fold	a.23 — Open three-helical up-and-down bundle
Superfamily Superfamily superfamily	a.23.3 — Methane monooxygenase hydrolase, gamma subunit
Family Family family	a.23.3.1 — Methane monooxygenase hydrolase, gamma subunit

Domain ID domain_id	d6ydig_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.137 — Monooxygenase (hydroxylase) regulatory protein
Superfamily Superfamily superfamily	d.137.1 — Monooxygenase (hydroxylase) regulatory protein
Family Family family	d.137.1.1 — Monooxygenase (hydroxylase) regulatory protein

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Unit-cell length a length_a	106.946 Å
Unit-cell length b length_b	106.946 Å
Unit-cell length c length_c	303.989 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 41 21 2
Space-group number int_tables_number	92
Crystal system crystal_system	tetragonal

Resolution resolution	1.950 Å
Low-resolution limit resolution_low	33.710 Å
R factor r_factor	0.1757
R_work r_work	0.1754
R_free r_free	0.1970

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

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

Methane monooxygenase

State in the Current Structure

Other States of the Same Protein in the Database

Methane monooxygenase component A alpha chain

State in the Current Structure

Other States of the Same Protein in the Database

Methane monooxygenase

State in the Current Structure

Other States of the Same Protein in the Database

Methane monooxygenase regulatory protein B

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

6ydi__assembly_1__model_1

6ydi__assembly_1__model_1 | I(q)

6ydi__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (7)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 polymer

Polymer Polymer

Source Source

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (4 domains)

7. Citations (1)

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

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

Methane monooxygenase

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Methane monooxygenase component A alpha chain

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Methane monooxygenase

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Methane monooxygenase regulatory protein B

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

6ydi__assembly_1__model_1

6ydi__assembly_1__model_1 | I(q)

6ydi__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (7)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 polymer

Polymer Polymer

Source Source

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (4 domains)

7. Citations (1)