2mta

CRYSTAL STRUCTURE OF A TERNARY ELECTRON TRANSFER COMPLEX BETWEEN METHYLAMINE DEHYDROGENASE, AMICYANIN AND A C-TYPE CYTOCHROME

Method: X-RAY DIFFRACTION

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

METHYLAMINE DEHYDROGENASE (HEAVY SUBUNIT)

Paracoccus denitrificans

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 8	METHYLAMINE DEHYDROGENASE (LIGHT SUBUNIT) × 2 （P22619） AMICYANIN × 2 （P22364） CYTOCHROME C551I × 2 （P29899） PHOSPHATE ION × 2 COPPER (II) ION × 2 HEME C × 2 water × 8	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	DHMH_PARDE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain H； PDBConstruct 1–373； UniProt 45–417

METHYLAMINE DEHYDROGENASE (LIGHT SUBUNIT)

Paracoccus denitrificans

UniProt P22619

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 8	METHYLAMINE DEHYDROGENASE (HEAVY SUBUNIT) × 2 （P29894） AMICYANIN × 2 （P22364） CYTOCHROME C551I × 2 （P29899） PHOSPHATE ION × 2 COPPER (II) ION × 2 HEME C × 2 water × 8	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	DHML_PARDE
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain L； PDBConstruct 1–125； UniProt 64–188

AMICYANIN

Paracoccus denitrificans

UniProt P22364

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 8	METHYLAMINE DEHYDROGENASE (HEAVY SUBUNIT) × 2 （P29894） METHYLAMINE DEHYDROGENASE (LIGHT SUBUNIT) × 2 （P22619） CYTOCHROME C551I × 2 （P29899） PHOSPHATE ION × 2 COPPER (II) ION × 2 HEME C × 2 water × 8	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	AMCY_PARDE
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain A； PDBConstruct 1–105； UniProt 27–131

CYTOCHROME C551I

Paracoccus denitrificans

UniProt P29899

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 8	METHYLAMINE DEHYDROGENASE (HEAVY SUBUNIT) × 2 （P29894） METHYLAMINE DEHYDROGENASE (LIGHT SUBUNIT) × 2 （P22619） AMICYANIN × 2 （P22364） PHOSPHATE ION × 2 COPPER (II) ION × 2 HEME C × 2 water × 8	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CYCL_PARDE
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain C； PDBConstruct 1–147； UniProt 23–169

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	2mta
Deposition date deposition_date	1993-10-26
Structure title title	CRYSTAL STRUCTURE OF A TERNARY ELECTRON TRANSFER COMPLEX BETWEEN METHYLAMINE DEHYDROGENASE, AMICYANIN AND A C-TYPE CYTOCHROME
Keywords keywords	ELECTRON TRANSPORT; ELECTRON TRANSPORT
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.

2mta__assembly_1__model_1

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

Download this curve (.dat)

2mta__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2mta__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	40.37 Å
Rg (electron density)	40.62 Å
Total Rg	40.72 Å
Atom count	11707
Residues	1498
Excluded volume	206130 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2mta__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 (8)

Entity 1 Entity 1 polymer

Description description	METHYLAMINE DEHYDROGENASE (HEAVY SUBUNIT)
Molecular weight formula_weight	41063.9 kDa
EC 编号 ec_number	1.4.99.3
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	H
Atom count atom_count	5981

QGQAAARAAAADLAAGQDDEPRILEAPAPDARRVYVNDPAHFAAVTQQFVIDGEAGRVIGMIDGGFLPNPVVADDGSFIAHASTVFSRIARGERTDYVEVFDPVTLLPTADIELPDAPRFLVGTYPWMTSLTPDGKTLLFYQFSPAPAVGVVDLEGKAFKRMLDVPDCYHIFPTAPDTFFMHCRDGSLAKVAFGTEGTPEITHTEVFHPEDEFLINHPAYSQKAGRLVWPTYTGKIHQIDLSSGDAKFLPAVEALTEAERADGWRPGGWQQVAYHRALDRIYLLVDQRDEWRHKTASRFLVVLDAKTGERLAKFEMGHEIDSINVSQDEKPLLYALSTGDKTLYIHDAESGEELRSVNQLGHGPQVITTADMG

Source Source

Source organism organism	Paracoccus denitrificans
NCBI taxonomy ID ncbi_taxonomy_id	266

Entity 2 Entity 2 polymer

Description description	METHYLAMINE DEHYDROGENASE (LIGHT SUBUNIT)
Molecular weight formula_weight	13728.2 kDa
EC 编号 ec_number	1.4.99.3
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	L

TDPRAKWVPQDNDIQACDYWRHCSIDGNICDCSGGSLTNCPPGTKLATASWVASCYNPTDGQSYLIAYRDCCGYNVSGRCPCLNTEGELPVYRPEFANDIIWCFGAEDDAMTYHCTISPIVGKAS

Source Source

Source organism organism	Paracoccus denitrificans
NCBI taxonomy ID ncbi_taxonomy_id	266

Entity 3 Entity 3 polymer

Description description	AMICYANIN
Molecular weight formula_weight	11505.2 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A

DKATIPSESPFAAAEVADGAIVVDIAKMKYETPELHVKVGDTVTWINREAMPHNVHFVAGVLGEAALKGPMMKKEQAYSLTFTEAGTYDYHCTPHPFMRGKVVVE

Source Source

Source organism organism	Paracoccus denitrificans
NCBI taxonomy ID ncbi_taxonomy_id	266

Entity 4 Entity 4 polymer

Description description	CYTOCHROME C551I
Molecular weight formula_weight	16274.9 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

APQFFNIIDGSPLNFDDAMEEGRDTEAVKHFLETGENVYNEDPEILPEAEELYAGMCSGCHGHYAEGKIGPGLNDAYWTYPGNETDVGLFSTLYGGATGQMGPMWGSLTLDEMLRTMAWVRHLYTGDPKDASWLTDEQKAGFTPFQP

Source Source

Source organism organism	Paracoccus denitrificans
NCBI taxonomy ID ncbi_taxonomy_id	266

Entity 5 Entity 5 non-polymer

Description description	PHOSPHATE ION
Molecular weight formula_weight	95.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 non-polymer

Description description	COPPER (II) ION
Molecular weight formula_weight	63.5 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 7 Entity 7 non-polymer

Description description	HEME C
Molecular weight formula_weight	618.5 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 8 Entity 8 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	127

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6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d2mtaa_
Class class	b — All beta proteins
Fold Fold fold	b.6 — Cupredoxin-like
Superfamily Superfamily superfamily	b.6.1 — Cupredoxins
Family Family family	b.6.1.1 — Plastocyanin/azurin-like

Domain ID domain_id	d2mtac_
Class class	a — All alpha proteins
Fold Fold fold	a.3 — Cytochrome c
Superfamily Superfamily superfamily	a.3.1 — Cytochrome c
Family Family family	a.3.1.1 — monodomain cytochrome c

Domain ID domain_id	d2mtah_
Class class	b — All beta proteins
Fold Fold fold	b.69 — 7-bladed beta-propeller
Superfamily Superfamily superfamily	b.69.2 — YVTN repeat-like/Quinoprotein amine dehydrogenase
Family Family family	b.69.2.1 — Methylamine dehydrogenase, H-chain

Domain ID domain_id	d2mtal_
Class class	g — Small proteins
Fold Fold fold	g.21 — Methylamine dehydrogenase, L chain
Superfamily Superfamily superfamily	g.21.1 — Methylamine dehydrogenase, L chain
Family Family family	g.21.1.1 — Methylamine dehydrogenase, L chain

CATH v4.4 (4 domains)

Domain ID domain_id	2mtaA00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	420 — Cupredoxins - blue copper proteins

Domain ID domain_id	2mtaC00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	760 — Cytochrome Bc1 Complex; Chain D, domain 2
Homologous superfamily homologous superfamily	10 — Cytochrome c-like domain

Domain ID domain_id	2mtaH00
Class class	2 — Mainly Beta
Architecture architecture	130 — 7 Propeller
Topology topology	10 — Methylamine Dehydrogenase; Chain H
Homologous superfamily homologous superfamily	10 — YVTN repeat-like/Quinoprotein amine dehydrogenase

Domain ID domain_id	2mtaL00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	30 — Electron Transport Ethylamine Dehydrogenase
Homologous superfamily homologous superfamily	10 — Methylamine/Aralkylamine dehydrogenase light chain

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Unit-cell length a length_a	148.810 Å
Unit-cell length b length_b	68.850 Å
Unit-cell length c length_c	187.180 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	C 2 2 21
Space-group number int_tables_number	20
Crystal system crystal_system	—

Resolution resolution	2.400 Å
Low-resolution limit resolution_low	— Å
R factor r_factor	0.1790
R_work r_work	0.1790
R_free r_free	—

CRYSTAL STRUCTURE OF A TERNARY ELECTRON TRANSFER COMPLEX BETWEEN METHYLAMINE DEHYDROGENASE, AMICYANIN AND A C-TYPE CYTOCHROME

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

METHYLAMINE DEHYDROGENASE (HEAVY SUBUNIT)

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

METHYLAMINE DEHYDROGENASE (LIGHT SUBUNIT)

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

AMICYANIN

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

CYTOCHROME C551I

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

2mta__assembly_1__model_1

2mta__assembly_1__model_1 | I(q)

2mta__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

5. Entities and Polymers Entities & Polymers (8)

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 water

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (5)