2d0v

Crystal structure of methanol dehydrogenase from Hyphomicrobium denitrificans

Method: X-RAY DIFFRACTION

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

methanol dehydrogenase large subunit

OrganismNot specified

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 small subunit × 2 （Q4AE23） CALCIUM ION × 2 PYRROLOQUINOLINE QUINONE × 2 water × 4	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 4	methanol dehydrogenase small subunit × 2 （Q4AE23） CALCIUM ION × 2 PYRROLOQUINOLINE QUINONE × 2 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q4AE26_9RHIZ
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–597； UniProt 1–597 Author chain D； PDBConstruct 1–597； UniProt 1–597 Author chain I； PDBConstruct 1–597； UniProt 1–597

methanol dehydrogenase small subunit

OrganismNot specified

UniProt Q4AE23

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 large subunit × 2 （Q4AE26） CALCIUM ION × 2 PYRROLOQUINOLINE QUINONE × 2 water × 4	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 4	methanol dehydrogenase large subunit × 2 （Q4AE26） CALCIUM ION × 2 PYRROLOQUINOLINE QUINONE × 2 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q4AE23_9RHIZ
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–72； UniProt 30–101 Author chain E； PDBConstruct 1–72； UniProt 30–101 Author chain J； PDBConstruct 1–72； UniProt 30–101

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	2d0v
Deposition date deposition_date	2005-08-09
Structure title title	Crystal structure of methanol dehydrogenase from Hyphomicrobium denitrificans
Keywords keywords	electron transfer, oxidoreductase, calcium binding, methanol, PQQ; 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.

2d0v__assembly_1__model_1

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

Download this curve (.dat)

2d0v__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2d0v__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	34.19 Å
Rg (electron density)	33.61 Å
Total Rg	34.18 Å
Atom count	10530
Residues	1334
Excluded volume	184970 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2d0v__assembly_1__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2d0v__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 (5)

Entity 1 Entity 1 polymer

Description description	methanol dehydrogenase large subunit
Molecular weight formula_weight	66173.6 kDa
EC 编号 ec_number	1.1.99.8
Source method src_method	nat
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,D,I
Atom count atom_count	16491

NDKLIELSNSNENWVMPGKNYDSNNYSTSTQINVDNVKQLKHAWSFSTGELHGHEGAPLVIGDVMYVHSSFPNKTFALDLNDPGHILWQHSPKQDPAARSVACCDLVNRGLAYWPGDDKTPSLIIKTQLDGHLVALNAKTGEEFWKVENGDIKVGQTLTQAPYVVHDLAIVGSSGAELGVRGHVTAYNVRTGEQAWRYYATGPDAEIGLADDFNSANPHYGQKGLGTATWEGDAWKIGGGTNWGWYAYDPAANLIYYGSGNPAPWNETMRPGDNKWTMTITARDADTGKMKFGYQKTPHDEWDFAGVNVIMLSEQTDKTGKKRKLLTHPDRNGIVYTLDRENGDLISADKLDDTVNVFKTVDLKTGLPVRDPEYGTRMDHKGTDICPSAMGYHNQGHDSYDPQKQLFFMGINHICMDWEPFMLPYRAGQFFVGATLWMYPGPKGDRQNYLGLGQIKAYNAITNEYKWQHMERFSVWGGTLATAGNLVFYGTLDGFLKARNSDTGELVWKHKLPSGVIGYPMTYEHKGVQYIAVMSGVGGWPGVGLVFDLQDPTAGLGAVGAFKNLQNYTQMGGSLEVFSLDGKNPYDDVNVGEYEKG

Entity 2 Entity 2 polymer

Description description	methanol dehydrogenase small subunit
Molecular weight formula_weight	8374.4 kDa
EC 编号 ec_number	1.1.99.8
Source method src_method	nat
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,E,J

YDGTHCKAPGNCWEPKPGFPEKIAGSKYDPKHDPKELNKQVESRKGEEERNANRAEHFKKTGKWVYDVKKIQ

Entity 3 Entity 3 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 4 Entity 4 non-polymer

Description description	PYRROLOQUINOLINE QUINONE
Molecular weight formula_weight	330.2 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	727

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6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

Domain ID domain_id	d2d0va_
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	d2d0vb_
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	d2d0vd_
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	d2d0ve_
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	d2d0vi_
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	d2d0vj_
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 (6 domains)

Domain ID domain_id	2d0vA00
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	2d0vB00
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	2d0vD00
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	2d0vE00
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	2d0vI00
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	2d0vJ00
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	291.320 Å
Unit-cell length b length_b	63.999 Å
Unit-cell length c length_c	109.941 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	105.74 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	12

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	2.490 Å
Low-resolution limit resolution_low	44.600 Å
R factor r_factor	0.1585
R_work r_work	0.1486
R_free r_free	0.2469

Crystal structure of methanol dehydrogenase from Hyphomicrobium denitrificans

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

methanol dehydrogenase large subunit

State in the Current Structure

Other States of the Same Protein in the Database

methanol dehydrogenase small subunit

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

2d0v__assembly_1__model_1

2d0v__assembly_1__model_1 | I(q)

2d0v__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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

CATH v4.4 (6 domains)

7. Citations (1)

Crystal structure of methanol dehydrogenase from Hyphomicrobium denitrificans

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

methanol dehydrogenase large 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

methanol dehydrogenase small 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

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

2d0v__assembly_1__model_1

2d0v__assembly_1__model_1 | I(q)

2d0v__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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

CATH v4.4 (6 domains)

7. Citations (1)