1yqw

Structure of the Oxidized Unready Form of Ni-Fe Hydrogenase

Method: X-RAY DIFFRACTION

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

Periplasmic [NiFe] hydrogenase small subunit

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	Periplasmic [NiFe] hydrogenase large subunit × 1 （P18188） IRON/SULFUR CLUSTER × 2 FE3-S4 CLUSTER × 1 GLYCEROL × 7 NICKEL (II) ION × 1 FE (II) ION × 1 BICARBONATE ION × 1 MAGNESIUM ION × 2 CARBONMONOXIDE-(DICYANO) IRON × 1 PEROXIDE ION × 1 water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	Periplasmic [NiFe] hydrogenase large subunit × 1 （P18188） IRON/SULFUR CLUSTER × 2 FE3-S4 CLUSTER × 1 GLYCEROL × 7 NICKEL (II) ION × 1 FE (II) ION × 1 MAGNESIUM ION × 1 CARBONMONOXIDE-(DICYANO) IRON × 1 PEROXIDE ION × 1 water × 2	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 2	Periplasmic [NiFe] hydrogenase large subunit × 1 （P18188） IRON/SULFUR CLUSTER × 2 FE3-S4 CLUSTER × 1 GLYCEROL × 3 NICKEL (II) ION × 1 FE (II) ION × 1 CARBONMONOXIDE-(DICYANO) IRON × 1 PEROXIDE ION × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PHNS_DESFR
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–264； UniProt 51–314 Author chain B； PDBConstruct 1–264； UniProt 51–314 Author chain C； PDBConstruct 1–264； UniProt 51–314

Periplasmic [NiFe] hydrogenase large subunit

OrganismNot specified

UniProt P18188

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Periplasmic [NiFe] hydrogenase small subunit × 1 （P18187） IRON/SULFUR CLUSTER × 2 FE3-S4 CLUSTER × 1 GLYCEROL × 7 NICKEL (II) ION × 1 FE (II) ION × 1 BICARBONATE ION × 1 MAGNESIUM ION × 2 CARBONMONOXIDE-(DICYANO) IRON × 1 PEROXIDE ION × 1 water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	Periplasmic [NiFe] hydrogenase small subunit × 1 （P18187） IRON/SULFUR CLUSTER × 2 FE3-S4 CLUSTER × 1 GLYCEROL × 7 NICKEL (II) ION × 1 FE (II) ION × 1 MAGNESIUM ION × 1 CARBONMONOXIDE-(DICYANO) IRON × 1 PEROXIDE ION × 1 water × 2	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 2	Periplasmic [NiFe] hydrogenase small subunit × 1 （P18187） IRON/SULFUR CLUSTER × 2 FE3-S4 CLUSTER × 1 GLYCEROL × 3 NICKEL (II) ION × 1 FE (II) ION × 1 CARBONMONOXIDE-(DICYANO) IRON × 1 PEROXIDE ION × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PHNL_DESFR
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain Q； PDBConstruct 1–549； UniProt 1–549 Author chain R； PDBConstruct 1–549； UniProt 1–549 Author chain S； PDBConstruct 1–549； UniProt 1–549

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	1yqw
Deposition date deposition_date	2005-02-02
Structure title title	Structure of the Oxidized Unready Form of Ni-Fe Hydrogenase
Keywords keywords	NI-FE HYDROGENASE UNREADY STATE, 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.

1yqw__assembly_3__model_1

Assembly 3 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

1yqw__assembly_3__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1yqw__assembly_3__model_1 | P(r) · Pending

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

Rg（Guinier）	25.45 Å
Rg (electron density)	24.55 Å
Total Rg	25.37 Å
Atom count	6173
Residues	804
Excluded volume	110240 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1yqw__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1yqw__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`1yqw__assembly_3__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 (12)

Entity 1 Entity 1 polymer

Description description	Periplasmic [NiFe] hydrogenase small subunit
Molecular weight formula_weight	28347.3 kDa
EC 编号 ec_number	1.12.2.1
Source method src_method	nat
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C
Atom count atom_count	20497

LTAKHRPSVVWLHNAECTGCTEAAIRTIKPYIDALILDTISLDYQETIMAAAGEAAEAALHQALEGKDGYYLVVEGGLPTIDGGQWGMVAGHPMIETTKKAAAKAKGIICIGTCSAYGGVQKAKPNPSQAKGVSEALGVKTINIPGCPPNPINFVGAVVHVLTKGIPDLDENGRPKLFYGELVHDNCPRLPHFEASEFAPSFDSEEAKKGFCLYELGCKGPVTYNNCPKVLFNQVNWPVQAGHPCLGCSEPDFWDTMTPFYEQG

Entity 2 Entity 2 polymer

Description description	Periplasmic [NiFe] hydrogenase large subunit
Molecular weight formula_weight	59713.3 kDa
EC 编号 ec_number	1.12.2.1
Mutation mutation	S499A
Source method src_method	nat
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	Q,R,S

MAESKPTPQSTFTGPIVVDPITRIEGHLRIMVEVENGKVKDAWSSSQLFRGLEIILKGRDPRDAQHFTQRACGVCTYVHALASSRCVDDAVKVSIPANARMMRNLVMASQYLHDHLVHFYHLHALDWVDVTAALKADPNKAAKLAASIAPARPGNSAKALKAVQDKLKAFVESGQLGIFTNAYFLGGHKAYYLPPEVNLIATAHYLEALHMQVKAASAMAILGGKNPHTQFTVVGGCSNYQGLTKDPLANYLALSKEVCQFVNECYIPDLLAVAGFYKDWGGIGGTSNYLAFGEFATDDSSPSKHLATSQFPSGVITGRDLGKVDNVDLGAIYEDVKYSWYAPGGDGKHPYDGVTDPKYTKLDDKDHYSWMKAPRYKGKAMEVGPLARTFIAYAKGQPDFKKVVDMVLGKLSVPATALHSTLGRTAARGIETAIVCANMEKWIKEMADSGAKDNTLCAKWEMPEESKGVGLADAPRGALSHWIRIKGKKIDNFQLVVPATWNLGPRGAQGDKSPVEEALIGTPIADPKRPVEILRTVHAFDPCIACGVH

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	6

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	3

Entity 5 Entity 5 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	17

Entity 6 Entity 6 non-polymer

Description description	NICKEL (II) ION
Molecular weight formula_weight	58.7 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 7 Entity 7 non-polymer

Description description	FE (II) ION
Molecular weight formula_weight	55.8 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 8 Entity 8 non-polymer

Description description	BICARBONATE ION
Molecular weight formula_weight	61.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 9 Entity 9 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 10 Entity 10 non-polymer

Description description	CARBONMONOXIDE-(DICYANO) IRON
Molecular weight formula_weight	135.9 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 11 Entity 11 non-polymer

Description description	PEROXIDE ION
Molecular weight formula_weight	32.0 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 12 Entity 12 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	1848

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6. Fold Classification (SCOP + CATH) 15 domains

SCOP 2.08 (6 domains)

Domain ID domain_id	d1yqwa_
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	d1yqwb_
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	d1yqwc_
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	d1yqwq_
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	d1yqwr_
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	d1yqws_
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 (9 domains)

Domain ID domain_id	1yqwA01
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	1yqwA02
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	1yqwB01
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	1yqwB02
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	1yqwC01
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	1yqwC02
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	1yqwQ00
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	1yqwR00
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	1yqwS00
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	64.410 Å
Unit-cell length b length_b	99.700 Å
Unit-cell length c length_c	182.830 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	91.42 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	6

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

Resolution resolution	1.830 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.1482
R_work r_work	0.1463
R_free r_free	0.1847

Structure of the Oxidized Unready Form of Ni-Fe Hydrogenase

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

Periplasmic [NiFe] hydrogenase small subunit

State in the Current Structure

Other States of the Same Protein in the Database

Periplasmic [NiFe] hydrogenase large subunit

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

1yqw__assembly_3__model_1

1yqw__assembly_3__model_1 | I(q)

1yqw__assembly_3__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 (12)

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

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 non-polymer

Entity 9 Entity 9 non-polymer

Entity 10 Entity 10 non-polymer

Entity 11 Entity 11 non-polymer

Entity 12 Entity 12 water

6. Fold Classification (SCOP + CATH) 15 domains

SCOP 2.08 (6 domains)

CATH v4.4 (9 domains)

7. Citations (3)

Structure of the Oxidized Unready Form of Ni-Fe Hydrogenase

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

Periplasmic [NiFe] hydrogenase small subunit

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Periplasmic [NiFe] hydrogenase large subunit

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

1yqw__assembly_3__model_1

1yqw__assembly_3__model_1 | I(q)

1yqw__assembly_3__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 (12)

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

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 non-polymer

Entity 9 Entity 9 non-polymer

Entity 10 Entity 10 non-polymer

Entity 11 Entity 11 non-polymer

Entity 12 Entity 12 water

6. Fold Classification (SCOP + CATH) 15 domains

SCOP 2.08 (6 domains)

CATH v4.4 (9 domains)

7. Citations (3)