1h4j

Methylobacterium extorquens methanol dehydrogenase D303E mutant

Method: X-RAY DIFFRACTION

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

Methanol dehydrogenase [cytochrome c] subunit 1

Methylobacterium extorquens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	Methanol dehydrogenase [cytochrome c] subunit 2 × 2 （P14775） PYRROLOQUINOLINE QUINONE × 2 CALCIUM ION × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 4	Methanol dehydrogenase [cytochrome c] subunit 2 × 2 （P14775） PYRROLOQUINOLINE QUINONE × 2 CALCIUM ION × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	DHM1_METEA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–599； UniProt 28–626 Author chain C； PDBConstruct 1–599； UniProt 28–626 Author chain E； PDBConstruct 1–599； UniProt 28–626 Author chain G； PDBConstruct 1–599； UniProt 28–626

Methanol dehydrogenase [cytochrome c] subunit 2

Methylobacterium extorquens

UniProt P14775

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	Methanol dehydrogenase [cytochrome c] subunit 1 × 2 （P16027） PYRROLOQUINOLINE QUINONE × 2 CALCIUM ION × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 4	Methanol dehydrogenase [cytochrome c] subunit 1 × 2 （P16027） PYRROLOQUINOLINE QUINONE × 2 CALCIUM ION × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	DHM2_METEA
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–74； UniProt 23–96 Author chain D； PDBConstruct 1–74； UniProt 23–96 Author chain F； PDBConstruct 1–74； UniProt 23–96 Author chain H； PDBConstruct 1–74； UniProt 23–96

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	1h4j
Deposition date deposition_date	2001-05-11
Structure title title	Methylobacterium extorquens methanol dehydrogenase D303E mutant
Keywords keywords	OXIDOREDUCTASE, DEHYDROGENASE, QUINOPROTEIN; 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.

1h4j__assembly_1__model_1

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

Download this curve (.dat)

1h4j__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1h4j__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	34.60 Å
Rg (electron density)	33.99 Å
Total Rg	34.60 Å
Atom count	10454
Residues	1334
Excluded volume	184890 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1h4j__assembly_1__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1h4j__assembly_2__model_1`	tetrameric （4）	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 (4)

Entity 1 Entity 1 polymer

Description description	Methanol dehydrogenase [cytochrome c] subunit 1
Molecular weight formula_weight	65880.9 kDa
EC 编号 ec_number	1.1.2.7
Mutation mutation	D303E
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C,E,G
Atom count atom_count	20908

NDKLVELSKSDDNWVMPGKNYDSNNFSDLKQINKGNVKQLRPAWTFSTGLLNGHEGAPLVVDGKMYIHTSFPNNTFALGLDDPGTILWQDKPKQNPAARAVACCDLVNRGLAYWPGDGKTPALILKTQLDGNVAALNAETGETVWKVENSDIKVGSTLTIAPYVVKDKVIIGSSGAELGVRGYLTAYDVKTGEQVWRAYATGPDKDLLLASDFNIKNPHYGQKGLGTGTWEGDAWKIGGGTNWGWYAYDPGTNLIYFGTGNPAPWNETMRPGDNKWTMTIFGRDADTGEAKFGYQKTPHDEWEYAGVNVMMLSEQKDKDGKARKLLTHPDRNGIVYTLDRTDGALVSANKLDDTVNVFKSVDLKTGQPVRDPEYGTRMDHLAKDICPSAMGYHNQGHDSYDPKRELFFMGINHICMDWEPFMLPYRAGQFFVGATLNMYPGPKGDRQNYEGLGQIKAYNAITGDYKWEKMERFAVWGGTMATAGDLVFYGTLDGYLKARDSDTGDLLWKFKIPSGAIGYPMTYTHKGTQYVAIYYGVGGWPGVGLVFDLADPTAGLGAVGAFKKLANYTQMGGGVVVFSLDGKGPYDDPNVGEWKSAAK

Source Source

Source organism organism	Methylobacterium extorquens
NCBI taxonomy ID ncbi_taxonomy_id	408
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Methanol dehydrogenase [cytochrome c] subunit 2
Molecular weight formula_weight	8480.6 kDa
EC 编号 ec_number	1.1.2.7
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

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

YDGTKCKAAGNCWEPKPGFPEKIAGSKYDPKHDPKELNKQADSIKQMEERNKKRVENFKKTGKFEYDVAKISAN

Source Source

Source organism organism	Methylobacterium extorquens
NCBI taxonomy ID ncbi_taxonomy_id	408
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 non-polymer

Description description	PYRROLOQUINOLINE QUINONE
Molecular weight formula_weight	330.2 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 4 Entity 4 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	4

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6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

Domain ID domain_id	d1h4ja_
Class class	b — All beta proteins
Fold Fold fold	b.70 — 8-bladed beta-propeller
Superfamily Superfamily superfamily	b.70.1 — Quinoprotein alcohol dehydrogenase-like
Family Family family	b.70.1.1 — Quinoprotein alcohol dehydrogenase-like

Domain ID domain_id	d1h4jb_
Class class	a — All alpha proteins
Fold Fold fold	a.137 — Non-globular all-alpha subunits of globular proteins
Superfamily Superfamily superfamily	a.137.2 — Methanol dehydrogenase subunit
Family Family family	a.137.2.1 — Methanol dehydrogenase subunit

Domain ID domain_id	d1h4jc_
Class class	b — All beta proteins
Fold Fold fold	b.70 — 8-bladed beta-propeller
Superfamily Superfamily superfamily	b.70.1 — Quinoprotein alcohol dehydrogenase-like
Family Family family	b.70.1.1 — Quinoprotein alcohol dehydrogenase-like

Domain ID domain_id	d1h4jd_
Class class	a — All alpha proteins
Fold Fold fold	a.137 — Non-globular all-alpha subunits of globular proteins
Superfamily Superfamily superfamily	a.137.2 — Methanol dehydrogenase subunit
Family Family family	a.137.2.1 — Methanol dehydrogenase subunit

Domain ID domain_id	d1h4je_
Class class	b — All beta proteins
Fold Fold fold	b.70 — 8-bladed beta-propeller
Superfamily Superfamily superfamily	b.70.1 — Quinoprotein alcohol dehydrogenase-like
Family Family family	b.70.1.1 — Quinoprotein alcohol dehydrogenase-like

Domain ID domain_id	d1h4jf_
Class class	a — All alpha proteins
Fold Fold fold	a.137 — Non-globular all-alpha subunits of globular proteins
Superfamily Superfamily superfamily	a.137.2 — Methanol dehydrogenase subunit
Family Family family	a.137.2.1 — Methanol dehydrogenase subunit

Domain ID domain_id	d1h4jg_
Class class	b — All beta proteins
Fold Fold fold	b.70 — 8-bladed beta-propeller
Superfamily Superfamily superfamily	b.70.1 — Quinoprotein alcohol dehydrogenase-like
Family Family family	b.70.1.1 — Quinoprotein alcohol dehydrogenase-like

Domain ID domain_id	d1h4jh_
Class class	a — All alpha proteins
Fold Fold fold	a.137 — Non-globular all-alpha subunits of globular proteins
Superfamily Superfamily superfamily	a.137.2 — Methanol dehydrogenase subunit
Family Family family	a.137.2.1 — Methanol dehydrogenase subunit

CATH v4.4 (8 domains)

Domain ID domain_id	1h4jA00
Class class	2 — Mainly Beta
Architecture architecture	140 — 8 Propeller
Topology topology	10 — Methanol Dehydrogenase; Chain A
Homologous superfamily homologous superfamily	10 — Quinoprotein alcohol dehydrogenase-like superfamily

Domain ID domain_id	1h4jB00
Class class	4 — Few Secondary Structures
Architecture architecture	10 — Irregular
Topology topology	160 — Methanol Dehydrogenase; Chain B
Homologous superfamily homologous superfamily	10 — Methanol dehydrogenase, beta subunit

Domain ID domain_id	1h4jC00
Class class	2 — Mainly Beta
Architecture architecture	140 — 8 Propeller
Topology topology	10 — Methanol Dehydrogenase; Chain A
Homologous superfamily homologous superfamily	10 — Quinoprotein alcohol dehydrogenase-like superfamily

Domain ID domain_id	1h4jD00
Class class	4 — Few Secondary Structures
Architecture architecture	10 — Irregular
Topology topology	160 — Methanol Dehydrogenase; Chain B
Homologous superfamily homologous superfamily	10 — Methanol dehydrogenase, beta subunit

Domain ID domain_id	1h4jE00
Class class	2 — Mainly Beta
Architecture architecture	140 — 8 Propeller
Topology topology	10 — Methanol Dehydrogenase; Chain A
Homologous superfamily homologous superfamily	10 — Quinoprotein alcohol dehydrogenase-like superfamily

Domain ID domain_id	1h4jF00
Class class	4 — Few Secondary Structures
Architecture architecture	10 — Irregular
Topology topology	160 — Methanol Dehydrogenase; Chain B
Homologous superfamily homologous superfamily	10 — Methanol dehydrogenase, beta subunit

Domain ID domain_id	1h4jG00
Class class	2 — Mainly Beta
Architecture architecture	140 — 8 Propeller
Topology topology	10 — Methanol Dehydrogenase; Chain A
Homologous superfamily homologous superfamily	10 — Quinoprotein alcohol dehydrogenase-like superfamily

Domain ID domain_id	1h4jH00
Class class	4 — Few Secondary Structures
Architecture architecture	10 — Irregular
Topology topology	160 — Methanol Dehydrogenase; Chain B
Homologous superfamily homologous superfamily	10 — Methanol dehydrogenase, beta subunit

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Unit-cell length a length_a	101.850 Å
Unit-cell length b length_b	61.020 Å
Unit-cell length c length_c	212.680 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	92.83 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	3.000 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.1870
R_work r_work	0.1870
R_free r_free	0.2170

Methylobacterium extorquens methanol dehydrogenase D303E mutant

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

Methanol dehydrogenase [cytochrome c] subunit 1

State in the Current Structure

Other States of the Same Protein in the Database

Methanol dehydrogenase [cytochrome c] subunit 2

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

1h4j__assembly_1__model_1

1h4j__assembly_1__model_1 | I(q)

1h4j__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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

CATH v4.4 (8 domains)

7. Citations (1)

Methylobacterium extorquens methanol dehydrogenase D303E mutant

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

Methanol dehydrogenase [cytochrome c] subunit 1

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Methanol dehydrogenase [cytochrome c] subunit 2

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

1h4j__assembly_1__model_1

1h4j__assembly_1__model_1 | I(q)

1h4j__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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

CATH v4.4 (8 domains)

7. Citations (1)