1jqk

Crystal structure of carbon monoxide dehydrogenase from Rhodospirillum rubrum

Method: X-RAY DIFFRACTION

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

carbon monoxide dehydrogenase

OrganismNot specified

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	FE (II) ION × 2 IRON/SULFUR CLUSTER × 3 FE(3)-NI(1)-S(4) CLUSTER × 2 UNKNOWN ATOM OR ION × 2	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 2	FE (II) ION × 2 IRON/SULFUR CLUSTER × 3 FE(3)-NI(1)-S(4) CLUSTER × 2 UNKNOWN ATOM OR ION × 2	Consistent with protein count
3	Protein homooligomer	Homooligomer	Protein 2	FE (II) ION × 2 IRON/SULFUR CLUSTER × 3 FE(3)-NI(1)-S(4) CLUSTER × 2 UNKNOWN ATOM OR ION × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	COOS_RHORU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–639； UniProt 1–639 Author chain B； PDBConstruct 1–639； UniProt 1–639 Author chain C； PDBConstruct 1–639； UniProt 1–639 Author chain D； PDBConstruct 1–639； UniProt 1–639 Author chain E； PDBConstruct 1–639； UniProt 1–639 Author chain F； PDBConstruct 1–639； UniProt 1–639

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	1jqk
Deposition date deposition_date	2001-08-07
Structure title title	Crystal structure of carbon monoxide dehydrogenase from Rhodospirillum rubrum
Keywords keywords	Rossmann fold, 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.

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1jqk__assembly_1__model_1`	dimeric （2）	Excluded	—	—
	Exclusion reason： The source record does not identify the atom or ion element unambiguously, so a reliable calculation is not possible.
2	1	`1jqk__assembly_2__model_1`	dimeric （2）	Excluded	—	—
	Exclusion reason： The source record does not identify the atom or ion element unambiguously, so a reliable calculation is not possible.
3	1	`1jqk__assembly_3__model_1`	dimeric （2）	Excluded	—	—
	Exclusion reason： The source record does not identify the atom or ion element unambiguously, so a reliable calculation is not possible.

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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	carbon monoxide dehydrogenase
Molecular weight formula_weight	66928.0 kDa
EC 编号 ec_number	1.2.99.2
Source method src_method	nat
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F
Atom count atom_count	26898

MTHHDCAHCSSDACATEMLNLAEANSIETAWHRYEKQQPQCGFGSAGLCCRICLKGPCRIDPFGEGPKYGVCGADRDTIVARHLVRMIAAGTAAHSEHGRHIALAMQHISQGELHDYSIRDEAKLYAIAKTLGVATEGRGLLAIVGDLAAITLGDFQNQDYDKPCAWLAASLTPRRVKRLGDLGLLPHNIDASVAQTMSRTHVGCDADPTNLILGGLRVAMADLDGSMLATELSDALFGTPQPVVSAANLGVMKRGAVNIAVNGHNPMLSDIICDVAADLRDEAIAAGAAEGINIIGICCTGHEVMMRHGVPLATNYLSQELPILTGALEAMVVDVQCIMPSLPRIAECFHTQIITTDKHNKISGATHVPFDEHKAVETAKTIIRMAIAAFGRRDPNRVAIPAFKQKSIVGFSAEAVVAALAKVNADDPLKPLVDNVVNGNIQGIVLFVGCNTTKVQQDSAYVDLAKSLAKRNVLVLATGCAAGAFAKAGLMTSEATTQYAGEGLKGVLSAIGTAAGLGGPLPLVMHMGSCVDNSRAVALATALANKLGVDLSDLPLVASAPECMSEKALAIGSWAVTIGLPTHVGSVPPVIGSQIVTKLVTETAKDLVGGYFIVDTDPKSAGDKLYAAIQERRAGLGL

Entity 2 Entity 2 non-polymer

Description description	FE (II) ION
Molecular weight formula_weight	55.8 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 3 Entity 3 non-polymer

Description description	IRON/SULFUR CLUSTER
Molecular weight formula_weight	351.6 kDa
Source method src_method	syn
Copy count entity_count	9

Entity 4 Entity 4 non-polymer

Description description	FE(3)-NI(1)-S(4) CLUSTER
Molecular weight formula_weight	354.5 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 5 Entity 5 non-polymer

Description description	UNKNOWN ATOM OR ION
Source method src_method	syn
Copy count entity_count	6

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6. Fold Classification (SCOP + CATH) 24 domains

SCOP 2.08 (6 domains)

Domain ID domain_id	d1jqka_
Class class	e — Multi-domain proteins (alpha and beta)
Fold Fold fold	e.26 — Prismane protein-like
Superfamily Superfamily superfamily	e.26.1 — Prismane protein-like
Family Family family	e.26.1.2 — Carbon monoxide dehydrogenase

Domain ID domain_id	d1jqkb_
Class class	e — Multi-domain proteins (alpha and beta)
Fold Fold fold	e.26 — Prismane protein-like
Superfamily Superfamily superfamily	e.26.1 — Prismane protein-like
Family Family family	e.26.1.2 — Carbon monoxide dehydrogenase

Domain ID domain_id	d1jqkc_
Class class	e — Multi-domain proteins (alpha and beta)
Fold Fold fold	e.26 — Prismane protein-like
Superfamily Superfamily superfamily	e.26.1 — Prismane protein-like
Family Family family	e.26.1.2 — Carbon monoxide dehydrogenase

Domain ID domain_id	d1jqkd_
Class class	e — Multi-domain proteins (alpha and beta)
Fold Fold fold	e.26 — Prismane protein-like
Superfamily Superfamily superfamily	e.26.1 — Prismane protein-like
Family Family family	e.26.1.2 — Carbon monoxide dehydrogenase

Domain ID domain_id	d1jqke_
Class class	e — Multi-domain proteins (alpha and beta)
Fold Fold fold	e.26 — Prismane protein-like
Superfamily Superfamily superfamily	e.26.1 — Prismane protein-like
Family Family family	e.26.1.2 — Carbon monoxide dehydrogenase

Domain ID domain_id	d1jqkf_
Class class	e — Multi-domain proteins (alpha and beta)
Fold Fold fold	e.26 — Prismane protein-like
Superfamily Superfamily superfamily	e.26.1 — Prismane protein-like
Family Family family	e.26.1.2 — Carbon monoxide dehydrogenase

CATH v4.4 (18 domains)

Domain ID domain_id	1jqkA01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	2030 —

Domain ID domain_id	1jqkA02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	2030 —

Domain ID domain_id	1jqkA03
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1270 — Substrate Binding Domain Of Dnak; Chain:A; Domain 2
Homologous superfamily homologous superfamily	30 —

Domain ID domain_id	1jqkB01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	2030 —

Domain ID domain_id	1jqkB02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	2030 —

Domain ID domain_id	1jqkB03
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1270 — Substrate Binding Domain Of Dnak; Chain:A; Domain 2
Homologous superfamily homologous superfamily	30 —

Domain ID domain_id	1jqkC01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	2030 —

Domain ID domain_id	1jqkC02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	2030 —

Domain ID domain_id	1jqkC03
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1270 — Substrate Binding Domain Of Dnak; Chain:A; Domain 2
Homologous superfamily homologous superfamily	30 —

Domain ID domain_id	1jqkD01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	2030 —

Domain ID domain_id	1jqkD02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	2030 —

Domain ID domain_id	1jqkD03
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1270 — Substrate Binding Domain Of Dnak; Chain:A; Domain 2
Homologous superfamily homologous superfamily	30 —

Domain ID domain_id	1jqkE01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	2030 —

Domain ID domain_id	1jqkE02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	2030 —

Domain ID domain_id	1jqkE03
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1270 — Substrate Binding Domain Of Dnak; Chain:A; Domain 2
Homologous superfamily homologous superfamily	30 —

Domain ID domain_id	1jqkF01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	2030 —

Domain ID domain_id	1jqkF02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	2030 —

Domain ID domain_id	1jqkF03
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1270 — Substrate Binding Domain Of Dnak; Chain:A; Domain 2
Homologous superfamily homologous superfamily	30 —

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Unit-cell length a length_a	92.600 Å
Unit-cell length b length_b	200.100 Å
Unit-cell length c length_c	116.800 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	111.50 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	12

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

Resolution resolution	2.800 Å
Low-resolution limit resolution_low	100.000 Å
R factor r_factor	0.2590
R_work r_work	0.2570
R_free r_free	0.2870

Crystal structure of carbon monoxide dehydrogenase from Rhodospirillum rubrum

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

carbon monoxide dehydrogenase

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

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 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

6. Fold Classification (SCOP + CATH) 24 domains

SCOP 2.08 (6 domains)

CATH v4.4 (18 domains)

7. Citations (1)

Crystal structure of carbon monoxide dehydrogenase from Rhodospirillum rubrum

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

carbon monoxide dehydrogenase

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

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 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

6. Fold Classification (SCOP + CATH) 24 domains

SCOP 2.08 (6 domains)

CATH v4.4 (18 domains)

7. Citations (1)