2j56

X-ray reduced Paraccocus denitrificans methylamine dehydrogenase N- semiquinone in complex with amicyanin.

Method: X-RAY DIFFRACTION

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

AMICYANIN

OrganismNot specified

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 6	METHYLAMINE DEHYDROGENASE HEAVY CHAIN × 2 （P29894） METHYLAMINE DEHYDROGENASE LIGHT CHAIN × 2 （P22619） COPPER (II) ION × 2 GLYCEROL × 1 SODIUM ION × 2 water × 6	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	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–105； UniProt 27–131 Author chain B； PDBConstruct 1–105； UniProt 27–131

METHYLAMINE DEHYDROGENASE HEAVY CHAIN

OrganismNot specified

UniProt P29894

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 6	AMICYANIN × 2 （P22364） METHYLAMINE DEHYDROGENASE LIGHT CHAIN × 2 （P22619） COPPER (II) ION × 2 GLYCEROL × 1 SODIUM ION × 2 water × 6	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	2
Chains and sequence ranges	Author chain H； PDBConstruct 1–386； UniProt 32–417 Author chain J； PDBConstruct 1–386； UniProt 32–417

METHYLAMINE DEHYDROGENASE LIGHT CHAIN

OrganismNot specified

UniProt P22619

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 6	AMICYANIN × 2 （P22364） METHYLAMINE DEHYDROGENASE HEAVY CHAIN × 2 （P29894） COPPER (II) ION × 2 GLYCEROL × 1 SODIUM ION × 2 water × 6	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	3
Chains and sequence ranges	Author chain L； PDBConstruct 1–131； UniProt 58–188 Author chain M； PDBConstruct 1–131； UniProt 58–188

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	2j56
Deposition date deposition_date	2006-09-12
Structure title title	X-ray reduced Paraccocus denitrificans methylamine dehydrogenase N- semiquinone in complex with amicyanin.
Keywords keywords	OXIDOREDUCTASE, PERIPLASMIC, METAL-BINDING, ELECTRON TRANSPORT, SINGLE CRYSTAL MICROSPECTROPHOTOMETRY; 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.

2j56__assembly_1__model_1

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

Download this curve (.dat)

2j56__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2j56__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	32.83 Å
Rg (electron density)	32.20 Å
Total Rg	32.85 Å
Atom count	9350
Residues	1206
Excluded volume	165140 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2j56__assembly_1__model_1`	hexameric （6）	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	AMICYANIN
Molecular weight formula_weight	11505.2 kDa
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	10400

DKATIPSESPFAAAEVADGAIVVDIAKMKYETPELHVKVGDTVTWINREAMPHNVHFVAGVLGEAALKGPMMKKEQAYSLTFTEAGTYDYHCTPHPFMRGKVVVE

Entity 2 Entity 2 polymer

Description description	METHYLAMINE DEHYDROGENASE HEAVY CHAIN
Molecular weight formula_weight	42449.3 kDa
EC 编号 ec_number	1.4.99.3
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

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

QDAPEAETQAQETQGQAAARAAAADLAAGQDDEPRILEAPAPDARRVYVNDPAHFAAVTQQFVIDGEAGRVIGMIDGGFLPNPVVADDGSFIAHASTVFSRIARGERTDYVEVFDPVTLLPTADIELPDAPRFLVGTYPWMTSLTPDGKTLLFYQFSPAPAVGVVDLEGKAFKRMLDVPDCYHIFPTAPDTFFMHCRDGSLAKVAFGTEGTPEITHTEVFHPEDEFLINHPAYSQKAGRLVWPTYTGKIHQIDLSSGDAKFLPAVEALTEAERADGWRPGGWQQVAYHRALDRIYLLVDQRDEWRHKTASRFVVVLDAKTGERLAKFEMGHEIDSINVSQDEKPLLYALSTGDKTLYIHDAESGEELRSVNQLGHGPQVITTADMG

Entity 3 Entity 3 polymer

Description description	METHYLAMINE DEHYDROGENASE LIGHT CHAIN
Molecular weight formula_weight	14209.7 kDa
EC 编号 ec_number	1.4.99.3
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	L,M

ADAPAGTDPRAKWVPQDNDIQACDYWRHCSIDGNICDCSGGSLTNCPPGTKLATASWVASCYNPTDGQSYLIAYRDCCGYNVSGRCPCLNTEGELPVYRPEFANDIIWCFGAEDDAMTYHCTISPIVGKAS

Entity 4 Entity 4 non-polymer

Description description	COPPER (II) ION
Molecular weight formula_weight	63.5 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 non-polymer

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

Entity 6 Entity 6 non-polymer

Description description	SODIUM ION
Molecular weight formula_weight	23.0 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	1033

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6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

Domain ID domain_id	d2j56a_
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	d2j56b_
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	d2j56h_
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.69.2.0 — automated matches

Domain ID domain_id	d2j56j_
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.69.2.0 — automated matches

Domain ID domain_id	d2j56l_
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

Domain ID domain_id	d2j56m_
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 (6 domains)

Domain ID domain_id	2j56A00
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	2j56B00
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	2j56H00
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	2j56J00
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	2j56L00
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

Domain ID domain_id	2j56M00
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	123.029 Å
Unit-cell length b length_b	123.029 Å
Unit-cell length c length_c	245.303 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	16

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

Resolution resolution	2.100 Å
Low-resolution limit resolution_low	43.480 Å
R factor r_factor	0.1710
R_work r_work	0.1690
R_free r_free	0.2070

X-ray reduced Paraccocus denitrificans methylamine dehydrogenase N- semiquinone in complex with amicyanin.

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

AMICYANIN

State in the Current Structure

Other States of the Same Protein in the Database

METHYLAMINE DEHYDROGENASE HEAVY CHAIN

State in the Current Structure

Other States of the Same Protein in the Database

METHYLAMINE DEHYDROGENASE LIGHT CHAIN

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

2j56__assembly_1__model_1

2j56__assembly_1__model_1 | I(q)

2j56__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 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 water

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

CATH v4.4 (6 domains)

7. Citations (2)

X-ray reduced Paraccocus denitrificans methylamine dehydrogenase N- semiquinone in complex with amicyanin.

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

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

METHYLAMINE DEHYDROGENASE HEAVY 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

METHYLAMINE DEHYDROGENASE LIGHT 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

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

2j56__assembly_1__model_1

2j56__assembly_1__model_1 | I(q)

2j56__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 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 water

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

CATH v4.4 (6 domains)

7. Citations (2)