SAXSdb — 5byq

▼

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

Iron hydrogenase 1

Clostridium pasteurianum

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	IRON/SULFUR CLUSTER × 4 FE2/S2 (INORGANIC) CLUSTER × 1 bis(cyanido-kappaC)(dicarbonyl)-mu-(oxomethylidene)-mu-(oxydimethanethiolate-1kappaS:2kappaS)diiron(2+) × 1 MAGNESIUM ION × 2 GLYCEROL × 1 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	IRON/SULFUR CLUSTER × 4 FE2/S2 (INORGANIC) CLUSTER × 1 bis(cyanido-kappaC)(dicarbonyl)-mu-(oxomethylidene)-mu-(oxydimethanethiolate-1kappaS:2kappaS)diiron(2+) × 1 MAGNESIUM ION × 2 GLYCEROL × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PHF1_CLOPA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–574； UniProt 1–574 Author chain B； PDBConstruct 1–574； UniProt 1–574

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	5byq
Deposition date deposition_date	2015-06-10
Structure title title	Semisynthetic [FeFe]-hydrogenase CpI with oxodithiolato-bridged [2Fe] cofactor
Keywords keywords	Hydrogenase, H-cluster, OXIDOREDUCTASE, semisynthetic enzyme; OXIDOREDUCTASE
Experimental Method method	X-RAY DIFFRACTION

▼

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.

5byq__assembly_1__model_1

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

Download this curve (.dat)

5byq__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5byq__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	25.56 Å
Rg (electron density)	25.03 Å
Total Rg	25.36 Å
Atom count	9030
Residues	580
Excluded volume	81557 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5byq__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`5byq__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (7)

Entity 1 Entity 1 polymer

Description description	Iron hydrogenase 1
Molecular weight formula_weight	65111.4 kDa
EC 编号 ec_number	1.12.7.2
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	18886

MKTIIINGVQFNTDEDTTILKFARDNNIDISALCFLNNCNNDINKCEICTVEVEGTGLVTACDTLIEDGMIINTNSDAVNEKIKSRISQLLDIHEFKCGPCNRRENCEFLKLVIKYKARASKPFLPKDKTEYVDERSKSLTVDRTKCLLCGRCVNACGKNTETYAMKFLNKNGKTIIGAEDEKCFDDTNCLLCGQCIIACPVAALSEKSHMDRVKNALNAPEKHVIVAMAPSVRASIGELFNMGFGVDVTGKIYTALRQLGFDKIFDINFGADMTIMEEATELVQRIENNGPFPMFTSCCPGWVRQAENYYPELLNNLSSAKSPQQIFGTASKTYYPSISGLDPKNVFTVTVMPCTSKKFEADRPQMEKDGLRDIDAVITTRELAKMIKDAKIPFAKLEDSEADPAMGEYSGAGAIFGATGGVMEAALRSAKDFAENAELEDIEYKQVRGLNGIKEAEVEINNNKYNVAVINGASNLFKFMKSGMINEKQYHFIEVMACHGGCVNGGGQPHVNPKDLEKVDIKKVRASVLYNQDEHLSKRKSHENTALVKMYQNYFGKPGEGRAHEILHFKYKKSAWSHPQFEK

Source Source

Source organism organism	Clostridium pasteurianum
NCBI taxonomy ID ncbi_taxonomy_id	1501
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	IRON/SULFUR CLUSTER
Molecular weight formula_weight	351.6 kDa
Source method src_method	syn
Copy count entity_count	8

Entity 3 Entity 3 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 4 Entity 4 non-polymer

Description description	bis(cyanido-kappaC)(dicarbonyl)-mu-(oxomethylidene)-mu-(oxydimethanethiolate-1kappaS:2kappaS)diiron(2+)
Molecular weight formula_weight	355.9 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 6 Entity 6 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 7 Entity 7 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	874

▼

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (8 domains)

Domain ID domain_id	d5byqa1
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.15.4.0 — automated matches

Domain ID domain_id	d5byqa2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.58 — Ferredoxin-like
Superfamily Superfamily superfamily	d.58.1 — 4Fe-4S ferredoxins
Family Family family	d.58.1.0 — automated matches

Domain ID domain_id	d5byqa3
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.96 — Fe-only hydrogenase
Superfamily Superfamily superfamily	c.96.1 — Fe-only hydrogenase
Family Family family	c.96.1.1 — Fe-only hydrogenase

Domain ID domain_id	d5byqa4
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d5byqb1
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.15.4.0 — automated matches

Domain ID domain_id	d5byqb2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.58 — Ferredoxin-like
Superfamily Superfamily superfamily	d.58.1 — 4Fe-4S ferredoxins
Family Family family	d.58.1.0 — automated matches

Domain ID domain_id	d5byqb3
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.96 — Fe-only hydrogenase
Superfamily Superfamily superfamily	c.96.1 — Fe-only hydrogenase
Family Family family	c.96.1.1 — Fe-only hydrogenase

Domain ID domain_id	d5byqb4
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

CATH v4.4 (4 domains)

Domain ID domain_id	5byqA01
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily	740 —

Domain ID domain_id	5byqA02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	5byqB01
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily	740 —

Domain ID domain_id	5byqB02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	20 —

▶

Unit-cell length a length_a	89.660 Å
Unit-cell length b length_b	72.450 Å
Unit-cell length c length_c	102.940 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	96.76 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

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

Resolution resolution	1.730 Å
Low-resolution limit resolution_low	47.770 Å
R factor r_factor	0.1467
R_work r_work	0.1464
R_free r_free	0.1756

Semisynthetic [FeFe]-hydrogenase CpI with oxodithiolato-bridged [2Fe] cofactor

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

Iron hydrogenase 1

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

5byq__assembly_1__model_1

5byq__assembly_1__model_1 | I(q)

5byq__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 (7)

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 non-polymer

Entity 7 Entity 7 water

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (8 domains)

CATH v4.4 (4 domains)

7. Citations (1)

Semisynthetic [FeFe]-hydrogenase CpI with oxodithiolato-bridged [2Fe] cofactor

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

Iron hydrogenase 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

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

5byq__assembly_1__model_1

5byq__assembly_1__model_1 | I(q)

5byq__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 (7)

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 non-polymer

Entity 7 Entity 7 water

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (8 domains)

CATH v4.4 (4 domains)

7. Citations (1)