SAXSdb — 1frv

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

HYDROGENASE

OrganismNot specified

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	HYDROGENASE × 1 （P12944） IRON/SULFUR CLUSTER × 2 FE3-S4 CLUSTER × 1 NICKEL (II) ION × 1 HYDRATED FE × 1	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	HYDROGENASE × 1 （P12944） IRON/SULFUR CLUSTER × 2 FE3-S4 CLUSTER × 1 NICKEL (II) ION × 1 HYDRATED FE × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PHNS_DESGI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–264； UniProt 25–288 Author chain C； PDBConstruct 1–264； UniProt 25–288

HYDROGENASE

OrganismNot specified

UniProt P12944

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	HYDROGENASE × 1 （P12943） IRON/SULFUR CLUSTER × 2 FE3-S4 CLUSTER × 1 NICKEL (II) ION × 1 HYDRATED FE × 1	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	HYDROGENASE × 1 （P12943） IRON/SULFUR CLUSTER × 2 FE3-S4 CLUSTER × 1 NICKEL (II) ION × 1 HYDRATED FE × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PHNL_DESGI
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 2–536； UniProt 1–535 Author chain D； PDBConstruct 2–536； UniProt 1–535

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	1frv
Deposition date deposition_date	1996-03-28
Structure title title	CRYSTAL STRUCTURE OF THE OXIDIZED FORM OF NI-FE HYDROGENASE
Keywords keywords	NI-FE HYDROGENASE, 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.

1frv__assembly_1__model_1

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

Download this curve (.dat)

1frv__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1frv__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	25.54 Å
Rg (electron density)	24.61 Å
Total Rg	25.38 Å
Atom count	6134
Residues	792
Excluded volume	109250 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1frv__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1frv__assembly_2__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	HYDROGENASE
Molecular weight formula_weight	28465.6 kDa
EC 编号 ec_number	1.12.2.1
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C
Atom count atom_count	12268

LTAKKRPSVVYLHNAECTGCSESLLRTVDPYVDELILDVISMDYHETLMAGAGHAVEEALHEAIKGDFVCVIEGGIPMGDGGYWGKVGRRNMYDICAEVAPKAKAVIAIGTCATYGGVQAAKPNPTGTVGVNEALGKLGVKAINIAGCPPNPMNFVGTVVHLLTKGMPELDKQGRPVMFFGETVHDNCPRLKHFEAGEFATSFGSPEAKKGYCLYELGCKGPDTYNNCPKQLFNQVNWPVQAGHPCIACSEPNFWDLYSPFYSA

Entity 2 Entity 2 polymer

Description description	HYDROGENASE
Molecular weight formula_weight	59783.1 kDa
EC 编号 ec_number	1.12.2.1
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,D

MSEMQGNKIVVDPITRIEGHLRIEVEVEGGKIKNAWSMSTLFRGLEMILKGRDPRDAQHFTQRACGVCTYVHALASVRAVDNCVGVKIPENATLMRNLTMGAQYMHDHLVHFYHLHALDWVNVANALNADPAKAARLANDLSPRKTTTESLKAVQAKVKALVESGQLGIFTNAYFLGGHPAYVLPAEVDLIATAHYLEALRVQVKAARAMAIFGAKNPHTQFTVVGGCTNYDSLRPERIAEFRKLYKEVREFIEQVYITDLLAVAGFYKNWAGIGKTSNFLTCGEFPTDEYDLNSRYTPQGVIWGNDLSKVDDFNPDLIEEHVKYSWYEGADAHHPYKGVTKPKWTEFHGEDRYSWMKAPRYKGEAFEVGPLASVLVAYAKKHEPTVKAVDLVLKTLGVGPEALFSTLGRTAARGIQCLTAAQEVEVWLDKLEANVKAGKDDLYTDWQYPTESQGVGFVNAPRGMLSHWIVQRGGKIENFQHVVPSTWNLGPRCAERKLSAVEQALIGTPIADPKRPVEILRTVHSYDPCIACGVH

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	4

Entity 4 Entity 4 non-polymer

Description description	FE3-S4 CLUSTER
Molecular weight formula_weight	295.8 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 non-polymer

Description description	NICKEL (II) ION
Molecular weight formula_weight	58.7 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 6 Entity 6 non-polymer

Description description	HYDRATED FE
Molecular weight formula_weight	109.9 kDa
Source method src_method	syn
Copy count entity_count	2

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6. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d1frva_
Class class	e — Multi-domain proteins (alpha and beta)
Fold Fold fold	e.19 — HydA/Nqo6-like
Superfamily Superfamily superfamily	e.19.1 — HydA/Nqo6-like
Family Family family	e.19.1.1 — Nickel-iron hydrogenase, small subunit

Domain ID domain_id	d1frvb_
Class class	e — Multi-domain proteins (alpha and beta)
Fold Fold fold	e.18 — HydB/Nqo4-like
Superfamily Superfamily superfamily	e.18.1 — HydB/Nqo4-like
Family Family family	e.18.1.1 — Nickel-iron hydrogenase, large subunit

Domain ID domain_id	d1frvc_
Class class	e — Multi-domain proteins (alpha and beta)
Fold Fold fold	e.19 — HydA/Nqo6-like
Superfamily Superfamily superfamily	e.19.1 — HydA/Nqo6-like
Family Family family	e.19.1.1 — Nickel-iron hydrogenase, small subunit

Domain ID domain_id	d1frvd_
Class class	e — Multi-domain proteins (alpha and beta)
Fold Fold fold	e.18 — HydB/Nqo4-like
Superfamily Superfamily superfamily	e.18.1 — HydB/Nqo4-like
Family Family family	e.18.1.1 — Nickel-iron hydrogenase, large subunit

CATH v4.4 (6 domains)

Domain ID domain_id	1frvA01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	700 — NADH:ubiquinone oxidoreductase-like, 20kDa subunit

Domain ID domain_id	1frvA02
Class class	4 — Few Secondary Structures
Architecture architecture	10 — Irregular
Topology topology	480 — Cytochrome-c3 Hydrogenase; Chain A, domain 2
Homologous superfamily homologous superfamily	10 — Cytochrome-c3 hydrogenase, C-terminal domain

Domain ID domain_id	1frvB00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	645 — Cytochrome-c3 Hydrogenase; chain B
Homologous superfamily homologous superfamily	10 — Cytochrome-c3 Hydrogenase, chain B

Domain ID domain_id	1frvC01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	700 — NADH:ubiquinone oxidoreductase-like, 20kDa subunit

Domain ID domain_id	1frvC02
Class class	4 — Few Secondary Structures
Architecture architecture	10 — Irregular
Topology topology	480 — Cytochrome-c3 Hydrogenase; Chain A, domain 2
Homologous superfamily homologous superfamily	10 — Cytochrome-c3 hydrogenase, C-terminal domain

Domain ID domain_id	1frvD00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	645 — Cytochrome-c3 Hydrogenase; chain B
Homologous superfamily homologous superfamily	10 — Cytochrome-c3 Hydrogenase, chain B

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Unit-cell length a length_a	63.600 Å
Unit-cell length b length_b	93.900 Å
Unit-cell length c length_c	69.200 Å
Unit-cell angle α angle_alpha	89.80 °
Unit-cell angle β angle_beta	102.90 °
Unit-cell angle γ angle_gamma	90.80 °
Molecules per unit cell Z z_pdb	2

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

Resolution resolution	2.850 Å
Low-resolution limit resolution_low	8.000 Å
R factor r_factor	—
R_work r_work	—
R_free r_free	—

CRYSTAL STRUCTURE OF THE OXIDIZED FORM OF NI-FE HYDROGENASE

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

HYDROGENASE

State in the Current Structure

Other States of the Same Protein in the Database

HYDROGENASE

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

1frv__assembly_1__model_1

1frv__assembly_1__model_1 | I(q)

1frv__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

Entity 2 Entity 2 polymer

Polymer 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

6. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (4 domains)

CATH v4.4 (6 domains)

7. Citations (3)

CRYSTAL STRUCTURE OF THE OXIDIZED FORM OF NI-FE HYDROGENASE

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

HYDROGENASE

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

HYDROGENASE

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

1frv__assembly_1__model_1

1frv__assembly_1__model_1 | I(q)

1frv__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

Entity 2 Entity 2 polymer

Polymer 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

6. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (4 domains)

CATH v4.4 (6 domains)

7. Citations (3)