7m8r

Complex structure of Methane monooxygenase hydroxylase and regulatory subunit with fluorosubstituted tryptophans

Method: X-RAY DIFFRACTION

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

Methane monooxygenase component A alpha chain

Methylosinus trichosporium OB3b

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 beta chain × 2 （A0A2D2D5X7） Methane monooxygenase gamma chain × 2 （A0A2D2D0T0） Methane monooxygenase regulatory protein B × 2 （A0A2D2D0T8） FE (III) ION × 4 1,2-ETHANEDIOL × 38 BENZOIC ACID × 2 1,1,1-tris(fluoranyl)propan-2-one × 2 CHLORIDE ION × 1 water × 8	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A0A2D2D5X0_METTR
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–515； UniProt 12–526 Author chain E； PDBConstruct 1–515； UniProt 12–526

Methane monooxygenase beta chain

Methylosinus trichosporium OB3b

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 （A0A2D2D5X0） Methane monooxygenase gamma chain × 2 （A0A2D2D0T0） Methane monooxygenase regulatory protein B × 2 （A0A2D2D0T8） FE (III) ION × 4 1,2-ETHANEDIOL × 38 BENZOIC ACID × 2 1,1,1-tris(fluoranyl)propan-2-one × 2 CHLORIDE ION × 1 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	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–392； UniProt 4–395 Author chain F； PDBConstruct 1–392； UniProt 4–395

Methane monooxygenase gamma chain

Methylosinus trichosporium OB3b

UniProt A0A2D2D0T0

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 （A0A2D2D5X0） Methane monooxygenase beta chain × 2 （A0A2D2D5X7） Methane monooxygenase regulatory protein B × 2 （A0A2D2D0T8） FE (III) ION × 4 1,2-ETHANEDIOL × 38 BENZOIC ACID × 2 1,1,1-tris(fluoranyl)propan-2-one × 2 CHLORIDE ION × 1 water × 8	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A0A2D2D0T0_METTR
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 1–168； UniProt 2–169 Author chain G； PDBConstruct 1–168； UniProt 2–169

Methane monooxygenase regulatory protein B

Methylosinus trichosporium OB3b

UniProt A0A2D2D0T8

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 （A0A2D2D5X0） Methane monooxygenase beta chain × 2 （A0A2D2D5X7） Methane monooxygenase gamma chain × 2 （A0A2D2D0T0） FE (III) ION × 4 1,2-ETHANEDIOL × 38 BENZOIC ACID × 2 1,1,1-tris(fluoranyl)propan-2-one × 2 CHLORIDE ION × 1 water × 8	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A0A2D2D0T8_METTR
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain D； PDBConstruct 1–136； UniProt 3–138 Author chain H； PDBConstruct 1–136； UniProt 3–138

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	7m8r
Deposition date deposition_date	2021-03-30
Structure title title	Complex structure of Methane monooxygenase hydroxylase and regulatory subunit with fluorosubstituted tryptophans
Keywords keywords	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.

7m8r__assembly_1__model_1

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

Download this curve (.dat)

7m8r__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

7m8r__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	40.59 Å
Rg (electron density)	40.27 Å
Total Rg	40.65 Å
Atom count	19650
Residues	2412
Excluded volume	347870 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`7m8r__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 (10)

Entity 1 Entity 1 polymer

Description description	Methane monooxygenase component A alpha chain
Molecular weight formula_weight	58971.0 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,E
Atom count atom_count	21512

DALKVNRAPVGVEPQEVHKWLQSFNWDFKENRTKYPTKYHMANETKEQFKVIAKEYARMEAAKDERQFGTLLDGLTRLGAGNKVHPRWGETMKVISNFLEVGEYNAIAASAMLWDSATAAEQKNGYLAQVLDEIRHTHQCAFINHYYSKHYHDPAGHNDARRTRAIGPLWKGMKRVFADGFISGDAVECSVNLQLVGEACFTNPLIVAVTEWASANGDEITPTVFLSVETDELRHMANGYQTVVSIANDPASAKFLNTDLNNAFWTQQKYFTPVLGYLFEYGSKFKVEPWVKTWNRWVYEDWGGIWIGRLGKYGVESPASLRDAKRDAYWAHHDLALAAYAMWPLGFARLALPDEEDQAWFEANYPGWADHYGKIFNEWKKLGYEDPKSGFIPYQWLLANGHDVYIDRVSQVPFIPSLAKGTGSLRVHEFNGKKHSLTDDWGERQWLIEPERYECHNVFEQYEGRELSEVIAEGHGVRSDGKTLIAQPHTRGDNLWTLEDIKRAGCVFPDPLAKF

Source Source

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

Entity 2 Entity 2 polymer

Description description	Methane monooxygenase beta chain
Molecular weight formula_weight	44948.9 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,F

PQSSQVTKRGLTDPERAAIIAAAVPDHALDTQRKYHYFIQPRWKRLSEYEQLSCYAQPNPDWIAGGLDWGDWTQKFHGGRPSWGNESTELRTTDWYRHRDPARRWHHPYVKDKSEEARYTQRFLAAYSSEGSIRTIDPYWRDEILNKYFGALLYSEYGLFNAHSSVGRDCLSDTIRQTAVFAALDKVDNAQMIQMERLFIAKLVPGFDASTDVPKKIWTTDPIYSGARATVQEIWQGVQDWNEILWAGHAVYDATFGQFARREFFQRLATVYGDTLTPFFTAQSQTYFQTTRGAIDDLFVYCLANDSEFGAHNRTFLNAWTEHYLASSVAALKDFVGLYAKVEKVAGATDRAGVSEALQRVFGDWKIDYADKIGFRVDVDQKVDAVLAGYKN

Source Source

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

Entity 3 Entity 3 polymer

Description description	Methane monooxygenase gamma chain
Molecular weight formula_weight	19313.2 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,G

AKREPIHDNSIRTEWEAKIAKLTSVDQATKFIQDFRLAYTSPFRKSYDIDVDYQYIERKIEEKLSVLKTEKLPVADLITKATTGEDAAAVEATWIAKIKAAKSKYEAERIHIEFRQLYKPPVLPVNVFLRTDAALGTVLMEIRNTDYYGTPLEGLRKERGVKVLHLQA

Source Source

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

Entity 4 Entity 4 polymer

Description description	Methane monooxygenase regulatory protein B
Molecular weight formula_weight	14688.6 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D,H

SAHNAYNAGIMQCTGKAFADEFFAEENQVVHESNAVVLVLMKSDEIDAIIEDIVLKGGKAKNPSIVVEDKAGFWWIKADGAIEIDAAEAGELLGKPFSVYDLLINVSSTVGRAYTLGTKFTITSELMGLDRALTDI

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	FE (III) ION
Molecular weight formula_weight	55.8 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 6 Entity 6 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	38

Entity 7 Entity 7 non-polymer

Description description	BENZOIC ACID
Molecular weight formula_weight	122.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 8 Entity 8 non-polymer

Description description	1,1,1-tris(fluoranyl)propan-2-one
Molecular weight formula_weight	112.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 9 Entity 9 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	nat
Copy count entity_count	1

Entity 10 Entity 10 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	1764

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6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (8 domains)

Domain ID domain_id	d7m8ra_
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	d7m8rb_
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	d7m8rc_
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	d7m8rd_
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

Domain ID domain_id	d7m8re_
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	d7m8rf_
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	d7m8rg_
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	d7m8rh_
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	102.388 Å
Unit-cell length b length_b	105.466 Å
Unit-cell length c length_c	298.184 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 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	orthorhombic

Resolution resolution	2.220 Å
Low-resolution limit resolution_low	86.100 Å
R factor r_factor	0.1590
R_work r_work	0.1570
R_free r_free	0.2020

Complex structure of Methane monooxygenase hydroxylase and regulatory subunit with fluorosubstituted tryptophans

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

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 beta 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 gamma 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 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

7m8r__assembly_1__model_1

7m8r__assembly_1__model_1 | I(q)

7m8r__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 (10)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

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 non-polymer

Entity 8 Entity 8 non-polymer

Entity 9 Entity 9 non-polymer

Entity 10 Entity 10 water

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (8 domains)

7. Citations (1)