1dgj

CRYSTAL STRUCTURE OF THE ALDEHYDE OXIDOREDUCTASE FROM DESULFOVIBRIO DESULFURICANS ATCC 27774

Method: X-RAY DIFFRACTION

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

ALDEHYDE OXIDOREDUCTASE

Desulfovibrio desulfuricans

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	FE2/S2 (INORGANIC) CLUSTER × 2 MOLYBDENUM (IV)OXIDE × 1 PTERIN CYTOSINE DINUCLEOTIDE × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q9REC4_DESDE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–907； UniProt 1–907

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	1dgj
Deposition date deposition_date	1999-11-24
Structure title title	CRYSTAL STRUCTURE OF THE ALDEHYDE OXIDOREDUCTASE FROM DESULFOVIBRIO DESULFURICANS ATCC 27774
Keywords keywords	BETA HALF-BARREL, FOUR-HELIX BUNDLE, BETA BARREL, 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.

1dgj__assembly_1__model_1

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

Download this curve (.dat)

1dgj__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1dgj__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	28.13 Å
Rg (electron density)	27.33 Å
Total Rg	28.12 Å
Atom count	6909
Residues	906
Excluded volume	122600 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1dgj__assembly_1__model_1`	monomeric （1）	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	ALDEHYDE OXIDOREDUCTASE
Molecular weight formula_weight	98017.8 kDa
EC 编号 ec_number	1.2.-.-
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	7102

METKTLIVNGMARRLLVSPNDLLVDVLRSQLQLTSVKVGCGKGQCGACTVILDGKVVRACIIKMSRVAENASVTTLEGIGAPDCLHPLQHAWIQHGAAQCGFCTPGFIVSAKALLDENVAPSREDVRDWFQKHHNICRCTGYKPLVDAVMDAAAILRGEKTVEEISFKMPADGRIWGSSIPRPSAVAKVTGLAEFGADAALRMPENTLHLALAQAKVSHALIKGIDTSEAEKMPGVYKVLTHKDVKGKNRITGLITFPTNKGDGWERPILNDSKIFQYGDALAIVCADSEANARAAAEKVKFDLELLPEYMSAPEAMAPDAIEIHPGTPNVYYDQLEEKGEDTVPFFNDPANVVAEGSYYTQRQPHLPIEPDVGYGYINEQGQVVIHSKSVAIHLHALMIAPGLGLEFPKDLVLVQNTTGGTFGYKFSPTMEALVGVAVMATGRPCHLRYNYEQQQNYTGKRSPFWTTMRYAADRQGKILAMETDWSVDHGPYSEFGDLLTLRGAQYIGAGYGIANIRGTGRTVATNHCWGAAFRGYGAPESEFPSEVLMDELAEKLGMDPFELRALNCYREGDTTSSGQIPEVMSLPEMFDKMRPYYEESKKRVKERSTAEIKRGVGVALGVYGAGLDGPDTSEAWVELNDDGSVTLGNSWEDHGQGADAGSLGTAHEALRPLGITPENIHLVMNDTSKTPNSGPAGGSRSQVVTGNAIRVACEMLIEGMRKPGGGFFTPAEMKAEGRPMRYDGKWTAPAKDCDAKGQGSPFACYMYGLFLTEVAVEVATGKATVEKMVCVADIGKICNKLVVDGQIYGGLAQGVGLALSEDYEDLKKHSTMGGAGIPSIKMIPDDIEIVYVETPRKDGPFGASGVGEMPLTAPHAAIINGIYNACGARVRHLPARPEKVLEAMPR

Source Source

Source organism organism	Desulfovibrio desulfuricans
NCBI taxonomy ID ncbi_taxonomy_id	876
Host organism host_organism	Bacteria

Entity 2 Entity 2 non-polymer

Description description	FE2/S2 (INORGANIC) CLUSTER
Molecular weight formula_weight	175.8 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	MOLYBDENUM (IV)OXIDE
Molecular weight formula_weight	127.9 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	PTERIN CYTOSINE DINUCLEOTIDE
Molecular weight formula_weight	696.5 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	193

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6. Fold Classification (SCOP + CATH) 11 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d1dgja1
Class class	a — All alpha proteins
Fold Fold fold	a.56 — CO dehydrogenase ISP C-domain like
Superfamily Superfamily superfamily	a.56.1 — CO dehydrogenase ISP C-domain like
Family Family family	a.56.1.1 — CO dehydrogenase ISP C-domain like

Domain ID domain_id	d1dgja2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.15 — beta-Grasp (ubiquitin-like)
Superfamily Superfamily superfamily	d.15.4 — 2Fe-2S ferredoxin-like
Family Family family	d.15.4.2 — 2Fe-2S ferredoxin domains from multidomain proteins

Domain ID domain_id	d1dgja3
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.41 — alpha/beta-Hammerhead
Superfamily Superfamily superfamily	d.41.1 — CO dehydrogenase molybdoprotein N-domain-like
Family Family family	d.41.1.1 — CO dehydrogenase molybdoprotein N-domain-like

Domain ID domain_id	d1dgja4
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.133 — Molybdenum cofactor-binding domain
Superfamily Superfamily superfamily	d.133.1 — Molybdenum cofactor-binding domain
Family Family family	d.133.1.1 — Molybdenum cofactor-binding domain

CATH v4.4 (7 domains)

Domain ID domain_id	1dgjA01
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily	30 — Beta-grasp domain

Domain ID domain_id	1dgjA02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	150 — DNA polymerase; domain 1
Homologous superfamily homologous superfamily	120 — [2Fe-2S]-binding domain

Domain ID domain_id	1dgjA03
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	1170 — Aldehyde Oxidoreductase; domain 3
Homologous superfamily homologous superfamily	50 — Aldehyde oxidase/xanthine dehydrogenase, a/b hammerhead

Domain ID domain_id	1dgjA04
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	365 — Aldehyde Oxidoreductase; domain 4
Homologous superfamily homologous superfamily	10 — Aldehyde oxidase/xanthine dehydrogenase, molybdopterin binding domain

Domain ID domain_id	1dgjA05
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	365 — Aldehyde Oxidoreductase; domain 4
Homologous superfamily homologous superfamily	10 — Aldehyde oxidase/xanthine dehydrogenase, molybdopterin binding domain

Domain ID domain_id	1dgjA06
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	365 — Aldehyde Oxidoreductase; domain 4
Homologous superfamily homologous superfamily	10 — Aldehyde oxidase/xanthine dehydrogenase, molybdopterin binding domain

Domain ID domain_id	1dgjA07
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	365 — Aldehyde Oxidoreductase; domain 4
Homologous superfamily homologous superfamily	10 — Aldehyde oxidase/xanthine dehydrogenase, molybdopterin binding domain

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Unit-cell length a length_a	156.639 Å
Unit-cell length b length_b	156.639 Å
Unit-cell length c length_c	177.149 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	12

Space group space_group	P 61 2 2
Space-group number int_tables_number	178
Crystal system crystal_system	—

Resolution resolution	2.800 Å
Low-resolution limit resolution_low	24.800 Å
R factor r_factor	0.1670
R_work r_work	0.1640
R_free r_free	0.2240

CRYSTAL STRUCTURE OF THE ALDEHYDE OXIDOREDUCTASE FROM DESULFOVIBRIO DESULFURICANS ATCC 27774

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

ALDEHYDE OXIDOREDUCTASE

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

1dgj__assembly_1__model_1

1dgj__assembly_1__model_1 | I(q)

1dgj__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

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 11 domains

SCOP 2.08 (4 domains)

CATH v4.4 (7 domains)

7. Citations (1)

CRYSTAL STRUCTURE OF THE ALDEHYDE OXIDOREDUCTASE FROM DESULFOVIBRIO DESULFURICANS ATCC 27774

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

ALDEHYDE OXIDOREDUCTASE

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

1dgj__assembly_1__model_1

1dgj__assembly_1__model_1 | I(q)

1dgj__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

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 11 domains

SCOP 2.08 (4 domains)

CATH v4.4 (7 domains)

7. Citations (1)