SAXSdb — 3b53

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

Carbon monoxide dehydrogenase 2

Carboxydothermus hydrogenoformans Z-2901

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 × 2 FE2/S2 (INORGANIC) CLUSTER × 2 FE(3)-NI(1)-S(4) CLUSTER × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	COOS2_CARHZ
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain X； PDBConstruct 24–656； UniProt 4–636

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	3b53
Deposition date deposition_date	2007-10-25
Structure title title	Ni,Fe-CODH-320 mV state
Keywords keywords	cluster C, 4Fe-4S, Cytoplasm, Iron, Iron-sulfur, Membrane, Metal-binding, Nickel, 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.

3b53__assembly_1__model_1

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

Download this curve (.dat)

3b53__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3b53__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	31.55 Å
Rg (electron density)	31.09 Å
Total Rg	31.36 Å
Atom count	9348
Residues	1266
Excluded volume	167760 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3b53__assembly_1__model_1`	dimeric （2）	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 (6)

Entity 1 Entity 1 polymer

Description description	Carbon monoxide dehydrogenase 2
Molecular weight formula_weight	69191.9 kDa
EC 编号 ec_number	1.2.99.2
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	X
Atom count atom_count	5654

MGSSHHHHHHSSGLVPRGSHMARQNLKSTDRAVQQMLDKAKREGIQTVWDRYEAMKPQCGFGETGLCCRHCLQGPCRINPFGDEPKVGICGATAEVIVARGLDRSIAAGAAGHSGHAKHLAHTLKKAVQGKAASYMIKDRTKLHSIAKRLGIPTEGQKDEDIALEVAKAALADFHEKDTPVLWVTTVLPPSRVKVLSAHGLIPAGIDHEIAEIMHRTSMGCDADAQNLLLGGLRCSLADLAGCYMGTDLADILFGTPAPVVTESNLGVLKADAVNVAVHGHNPVLSDIIVSVSKEMENEARAAGATGINVVGICCTGNEVLMRHGIPACTHSVSQEMAMITGALDAMILDYQCIQPSVATIAECTGTTVITTMEMSKITGATHVNFAEEAAVENAKQILRLAIDTFKRRKGKPVEIPNIKTKVVAGFSTEAIINALSKLNANDPLKPLIDNVVNGNIRGVCLFAGCNNVKVPQDQNFTTIARKLLKQNVLVVATGCGAGALMRHGFMDPANVDELCGDGLKAVLTAIGEANGLGGPLPPVLHMGSCVDNSRAVALVAALANRLGVDLDRLPVVASAAEAMHEKAVAIGTWAVTIGLPTHIGVLPPITGSLPVTQILTSSVKDITGGYFIVELDPETAADKLLAAINERRAGLGLPW

Source Source

Source organism organism	Carboxydothermus hydrogenoformans Z-2901
NCBI taxonomy ID ncbi_taxonomy_id	246194
Host organism host_organism	Escherichia coli

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	1

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	1

Entity 4 Entity 4 non-polymer

Description description	FE2/S2 (INORGANIC) CLUSTER
Molecular weight formula_weight	175.8 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 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	1

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	884

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6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d3b53x_
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 (3 domains)

Domain ID domain_id	3b53X01
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	3b53X02
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	3b53X03
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	2030 —

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Unit-cell length a length_a	111.830 Å
Unit-cell length b length_b	74.520 Å
Unit-cell length c length_c	70.740 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	111.40 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

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

Resolution resolution	1.500 Å
Low-resolution limit resolution_low	26.660 Å
R factor r_factor	0.1460
R_work r_work	0.1450
R_free r_free	0.1780

Ni,Fe-CODH-320 mV state

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

Carbon monoxide dehydrogenase 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

3b53__assembly_1__model_1

3b53__assembly_1__model_1 | I(q)

3b53__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 (6)

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 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (1 domains)

CATH v4.4 (3 domains)

7. Citations (1)

Ni,Fe-CODH-320 mV state

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

Carbon monoxide dehydrogenase 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

3b53__assembly_1__model_1

3b53__assembly_1__model_1 | I(q)

3b53__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 (6)

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 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (1 domains)

CATH v4.4 (3 domains)

7. Citations (1)