1hfe

1.6 A RESOLUTION STRUCTURE OF THE FE-ONLY HYDROGENASE FROM DESULFOVIBRIO DESULFURICANS

Method: X-RAY DIFFRACTION

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

PROTEIN (FE-ONLY HYDROGENASE (E.C.1.18.99.1) (SMALLER 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	PROTEIN (FE-ONLY HYDROGENASE (E.C.1.18.99.1) (LARGER SUBUNIT)) × 1 （P07598） ZINC ION × 1 FE (II) ION × 2 CYANIDE ION × 2 IRON/SULFUR CLUSTER × 3 1,3-PROPANEDITHIOL × 1 CARBON MONOXIDE × 2 CYSTEINE × 1 water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	PROTEIN (FE-ONLY HYDROGENASE (E.C.1.18.99.1) (LARGER SUBUNIT)) × 1 （P07598） FE (II) ION × 2 CYANIDE ION × 2 IRON/SULFUR CLUSTER × 3 1,3-PROPANEDITHIOL × 1 CARBON MONOXIDE × 2 CYSTEINE × 1 water × 2	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 4	PROTEIN (FE-ONLY HYDROGENASE (E.C.1.18.99.1) (LARGER SUBUNIT)) × 2 （P07598） ZINC ION × 1 FE (II) ION × 4 CYANIDE ION × 4 IRON/SULFUR CLUSTER × 6 1,3-PROPANEDITHIOL × 2 CARBON MONOXIDE × 4 CYSTEINE × 2 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PHFS_DESVH
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain S； PDBConstruct 1–123； UniProt 1–123 Author chain T； PDBConstruct 1–123； UniProt 1–123

PROTEIN (FE-ONLY HYDROGENASE (E.C.1.18.99.1) (LARGER SUBUNIT))

OrganismNot specified

UniProt P07598

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	PROTEIN (FE-ONLY HYDROGENASE (E.C.1.18.99.1) (SMALLER SUBUNIT)) × 1 （P07603） ZINC ION × 1 FE (II) ION × 2 CYANIDE ION × 2 IRON/SULFUR CLUSTER × 3 1,3-PROPANEDITHIOL × 1 CARBON MONOXIDE × 2 CYSTEINE × 1 water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	PROTEIN (FE-ONLY HYDROGENASE (E.C.1.18.99.1) (SMALLER SUBUNIT)) × 1 （P07603） FE (II) ION × 2 CYANIDE ION × 2 IRON/SULFUR CLUSTER × 3 1,3-PROPANEDITHIOL × 1 CARBON MONOXIDE × 2 CYSTEINE × 1 water × 2	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 4	PROTEIN (FE-ONLY HYDROGENASE (E.C.1.18.99.1) (SMALLER SUBUNIT)) × 2 （P07603） ZINC ION × 1 FE (II) ION × 4 CYANIDE ION × 4 IRON/SULFUR CLUSTER × 6 1,3-PROPANEDITHIOL × 2 CARBON MONOXIDE × 4 CYSTEINE × 2 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PHFL_DESVH
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain L； PDBConstruct 1–421； UniProt 1–421 Author chain M； PDBConstruct 1–421； UniProt 1–421

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	1hfe
Deposition date deposition_date	1998-11-11
Structure title title	1.6 A RESOLUTION STRUCTURE OF THE FE-ONLY HYDROGENASE FROM DESULFOVIBRIO DESULFURICANS
Keywords keywords	FE-ONLY HYDROGENASE, HYDROGENE METABOLISM, PERIPLASM, HYDROGENASE; HYDROGENASE
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.

1hfe__assembly_1__model_1

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

Download this curve (.dat)

1hfe__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1hfe__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	21.86 Å
Rg (electron density)	20.99 Å
Total Rg	21.70 Å
Atom count	3775
Residues	485
Excluded volume	67686 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1hfe__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1hfe__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`1hfe__assembly_3__model_1`	tetrameric （4）	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 (10)

Entity 1 Entity 1 polymer

Description description	PROTEIN (FE-ONLY HYDROGENASE (E.C.1.18.99.1) (SMALLER SUBUNIT))
Molecular weight formula_weight	13646.8 kDa
EC 编号 ec_number	1.18.99.1
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	S,T
Atom count atom_count	9079

MQIASITRRGFLKVACVTTGAALIGIRMTGKAVAAVKQIKDYMLDRINGVYGADAKFPVRASQDNTQVKALYKSYLEKPLGHKSHDLLHTHWFDKSKGVKELTTAGKLPNPRASEFEGPYPYE

Entity 2 Entity 2 polymer

Description description	PROTEIN (FE-ONLY HYDROGENASE (E.C.1.18.99.1) (LARGER SUBUNIT))
Molecular weight formula_weight	46011.1 kDa
EC 编号 ec_number	1.18.99.1
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	L,M

MSRTVMERIEYEMHTPDPKADPDKLHFVQIDEAKCIGCDTCSQYCPTAAIFGEMGEPHSIPHIEACINCGQCLTHCPENAIYEAQSWVPEVEKKLKDGKVKCIAMPAPAVRYALGDAFGMPVGSVTTGKMLAALQKLGFAHCWDTEFTADVTIWEEGSEFVERLTKKSDMPLPQFTSCCPGWQKYAETYYPELLPHFSTCKSPIGMNGALAKTYGAERMKYDPKQVYTVSIMPCIAKKYEGLRPELKSSGMRDIDATLTTRELAYMIKKAGIDFAKLPDGKRDSLMGESTGGATIFGVTGGVMEAALRFAYEAVTGKKPDSWDFKAVRGLDGIKEATVNVGGTDVKVAVVHGAKRFKQVCDDVKAGKSPYHFIEYMACPGGCVCGGGQPVMPGVLEAMDRTTTRLYAGLKKRLAMASANKA

Entity 3 Entity 3 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	FE (II) ION
Molecular weight formula_weight	55.8 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 5 Entity 5 non-polymer

Description description	CYANIDE ION
Molecular weight formula_weight	26.0 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 6 Entity 6 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 7 Entity 7 non-polymer

Description description	1,3-PROPANEDITHIOL
Molecular weight formula_weight	108.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 8 Entity 8 non-polymer

Description description	CARBON MONOXIDE
Molecular weight formula_weight	28.0 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 9 Entity 9 non-polymer

Description description	CYSTEINE
Molecular weight formula_weight	121.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 10 Entity 10 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	1179

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6. Fold Classification (SCOP + CATH) 14 domains

SCOP 2.08 (6 domains)

Domain ID domain_id	d1hfel1
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	d1hfel2
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.58.1.5 — Ferredoxin domains from multidomain proteins

Domain ID domain_id	d1hfem1
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	d1hfem2
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.58.1.5 — Ferredoxin domains from multidomain proteins

Domain ID domain_id	d1hfes_
Class class	a — All alpha proteins
Fold Fold fold	a.137 — Non-globular all-alpha subunits of globular proteins
Superfamily Superfamily superfamily	a.137.4 — Fe-only hydrogenase smaller subunit
Family Family family	a.137.4.1 — Fe-only hydrogenase smaller subunit

Domain ID domain_id	d1hfet_
Class class	a — All alpha proteins
Fold Fold fold	a.137 — Non-globular all-alpha subunits of globular proteins
Superfamily Superfamily superfamily	a.137.4 — Fe-only hydrogenase smaller subunit
Family Family family	a.137.4.1 — Fe-only hydrogenase smaller subunit

CATH v4.4 (8 domains)

Domain ID domain_id	1hfeL01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1780 —

Domain ID domain_id	1hfeL02
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	1hfeL03
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	950 — Fe-only Hydrogenase (Larger Subunit); Chain L, domain 3
Homologous superfamily homologous superfamily	10 — Fe-only Hydrogenase (Larger Subunit); Chain L, domain 3

Domain ID domain_id	1hfeM01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1780 —

Domain ID domain_id	1hfeM02
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	1hfeM03
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	950 — Fe-only Hydrogenase (Larger Subunit); Chain L, domain 3
Homologous superfamily homologous superfamily	10 — Fe-only Hydrogenase (Larger Subunit); Chain L, domain 3

Domain ID domain_id	1hfeS00
Class class	4 — Few Secondary Structures
Architecture architecture	10 — Irregular
Topology topology	260 — G Protein Gi Gamma 2
Homologous superfamily homologous superfamily	20 — Iron hydrogenase, small subunit

Domain ID domain_id	1hfeT00
Class class	4 — Few Secondary Structures
Architecture architecture	10 — Irregular
Topology topology	260 — G Protein Gi Gamma 2
Homologous superfamily homologous superfamily	20 — Iron hydrogenase, small subunit

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Unit-cell length a length_a	128.970 Å
Unit-cell length b length_b	123.070 Å
Unit-cell length c length_c	65.070 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 21 21 2
Space-group number int_tables_number	18
Crystal system crystal_system	—

Resolution resolution	1.600 Å
Low-resolution limit resolution_low	7.000 Å
R factor r_factor	—
R_work r_work	0.1582
R_free r_free	0.1820

1.6 A RESOLUTION STRUCTURE OF THE FE-ONLY HYDROGENASE FROM DESULFOVIBRIO DESULFURICANS

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

PROTEIN (FE-ONLY HYDROGENASE (E.C.1.18.99.1) (SMALLER SUBUNIT))

State in the Current Structure

Other States of the Same Protein in the Database

PROTEIN (FE-ONLY HYDROGENASE (E.C.1.18.99.1) (LARGER 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

1hfe__assembly_1__model_1

1hfe__assembly_1__model_1 | I(q)

1hfe__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 (10)

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 water

6. Fold Classification (SCOP + CATH) 14 domains

SCOP 2.08 (6 domains)

CATH v4.4 (8 domains)

7. Citations (1)

1.6 A RESOLUTION STRUCTURE OF THE FE-ONLY HYDROGENASE FROM DESULFOVIBRIO DESULFURICANS

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

PROTEIN (FE-ONLY HYDROGENASE (E.C.1.18.99.1) (SMALLER 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

PROTEIN (FE-ONLY HYDROGENASE (E.C.1.18.99.1) (LARGER 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

1hfe__assembly_1__model_1

1hfe__assembly_1__model_1 | I(q)

1hfe__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 (10)

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 water

6. Fold Classification (SCOP + CATH) 14 domains

SCOP 2.08 (6 domains)

CATH v4.4 (8 domains)

7. Citations (1)