4upe

Structure of the unready Ni-A state of the S499C mutant of D. fructosovorans NiFe-hydrogenase

Method: X-RAY DIFFRACTION

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

NIFE-HYDROGENASE SMALL SUBUNIT

DESULFOVIBRIO FRUCTOSOVORANS

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	NICKEL-DEPENDENT HYDROGENASE LARGE SUBUNIT × 1 （P18188） IRON/SULFUR CLUSTER × 2 FE3-S4 CLUSTER × 1 CARBONMONOXIDE-(DICYANO) IRON × 1 NICKEL (II) ION × 1 CALCIUM ION × 1 GLYCEROL × 2 PHOSPHATE ION × 1 water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	NICKEL-DEPENDENT HYDROGENASE LARGE SUBUNIT × 1 （P18188） IRON/SULFUR CLUSTER × 2 FE3-S4 CLUSTER × 1 CARBONMONOXIDE-(DICYANO) IRON × 1 NICKEL (II) ION × 1 CALCIUM ION × 2 GLYCEROL × 2 PHOSPHATE ION × 1 water × 2	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 2	NICKEL-DEPENDENT HYDROGENASE LARGE SUBUNIT × 1 （P18188） IRON/SULFUR CLUSTER × 2 FE3-S4 CLUSTER × 1 CARBONMONOXIDE-(DICYANO) IRON × 1 NICKEL (II) ION × 1 CALCIUM ION × 1 GLYCEROL × 1 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 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 1–265； UniProt 50–314 Author chain B； PDBConstruct 1–265； UniProt 50–314 Author chain C； PDBConstruct 1–265； UniProt 50–314

NICKEL-DEPENDENT HYDROGENASE LARGE SUBUNIT

DESULFOVIBRIO FRUCTOSOVORANS

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	NIFE-HYDROGENASE SMALL SUBUNIT × 1 （P18187） IRON/SULFUR CLUSTER × 2 FE3-S4 CLUSTER × 1 CARBONMONOXIDE-(DICYANO) IRON × 1 NICKEL (II) ION × 1 CALCIUM ION × 1 GLYCEROL × 2 PHOSPHATE ION × 1 water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	NIFE-HYDROGENASE SMALL SUBUNIT × 1 （P18187） IRON/SULFUR CLUSTER × 2 FE3-S4 CLUSTER × 1 CARBONMONOXIDE-(DICYANO) IRON × 1 NICKEL (II) ION × 1 CALCIUM ION × 2 GLYCEROL × 2 PHOSPHATE ION × 1 water × 2	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 2	NIFE-HYDROGENASE SMALL SUBUNIT × 1 （P18187） IRON/SULFUR CLUSTER × 2 FE3-S4 CLUSTER × 1 CARBONMONOXIDE-(DICYANO) IRON × 1 NICKEL (II) ION × 1 CALCIUM ION × 1 GLYCEROL × 1 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 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 1–548； UniProt 2–549 Author chain R； PDBConstruct 1–548； UniProt 2–549 Author chain S； PDBConstruct 1–548； UniProt 2–549

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	4upe
Deposition date deposition_date	2014-06-16
Structure title title	Structure of the unready Ni-A state of the S499C mutant of D. fructosovorans NiFe-hydrogenase
Keywords keywords	OXIDOREDUCTASE, NIFE-SITE, NI-A STATE, SULFENATE; 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.

4upe__assembly_2__model_1

Assembly 2 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

4upe__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4upe__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	25.58 Å
Rg (electron density)	24.67 Å
Total Rg	25.49 Å
Atom count	6190
Residues	805
Excluded volume	110560 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4upe__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`4upe__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`4upe__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 (11)

Entity 1 Entity 1 polymer

Description description	NIFE-HYDROGENASE SMALL SUBUNIT
Molecular weight formula_weight	28418.4 kDa
EC 编号 ec_number	1.12.2.1
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C
Atom count atom_count	20844

ALTAKHRPSVVWLHNAECTGCTEAAIRTIKPYIDALILDTISLDYQETIMAAAGEAAEAALHQALEGKDGYYLVVEGGLPTIDGGQWGMVAGHPMIETTKKAAAKAKGIICIGTCSAYGGVQKAKPNPSQAKGVSEALGVKTINIPGCPPNPINFVGAVVHVLTKGIPDLDENGRPKLFYGELVHDNCPRLPHFEASEFAPSFDSEEAKKGFCLYELGCKGPVTYNNCPKVLFNQVNWPVQAGHPCLGCSEPDFWDTMTPFYEQG

Source Source

Source organism organism	DESULFOVIBRIO FRUCTOSOVORANS
NCBI taxonomy ID ncbi_taxonomy_id	878
Host organism host_organism	DESULFOVIBRIO FRUCTOSOVORANS

Entity 2 Entity 2 polymer

Description description	NICKEL-DEPENDENT HYDROGENASE LARGE SUBUNIT
Molecular weight formula_weight	59673.2 kDa
EC 编号 ec_number	1.12.2.1
Mutation mutation	YES
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

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

AESKPTPQSTFTGPIVVDPITRIEGHLRIMVEVENGKVKDAWSSSQLFRGLEIILKGRDPRDAQHFTQRACGVCTYVHALASSRCVDDAVKVSIPANARMMRNLVMASQYLHDHLVHFYHLHALDWVDVTAALKADPNKAAKLAASIAPARPGNSAKALKAVQDKLKAFVESGQLGIFTNAYFLGGHKAYYLPPEVDLIATAHYLEALHMQVKAASAMAILGGKNPHTQFTVVGGCSNYQGLTKDPLANYLALSKEVCQFVNECYIPDLLAVAGFYKDWGGIGGTSNYLAFGEFATDDSSPEKHLATSQFPSGVITGRDLGKVDNVDLGAIYEDVKYSWYAPGGDGKHPYDGVTDPKYTKLDDKDHYSWMKAPRYKGKAMEVGPLARTFIAYAKGQPDFKKVVDMVLGKLSVPATALHSTLGRTAARGIETAIVCANMEKWIKEMADSGAKDNTLCAKWEMPEESKGVGLADAPRGALSHWIRIKGKKIDNFQLVVPCTWNLGPRGAQGDKSPVEEALIGTPIADPKRPVEILRTVHAFDPCIACGVH

Source Source

Source organism organism	DESULFOVIBRIO FRUCTOSOVORANS
NCBI taxonomy ID ncbi_taxonomy_id	878
Host organism host_organism	DESULFOVIBRIO FRUCTOSOVORANS

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

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	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 8 Entity 8 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	5

Entity 9 Entity 9 non-polymer

Description description	PHOSPHATE ION
Molecular weight formula_weight	95.0 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 10 Entity 10 non-polymer

Description description	2-(N-MORPHOLINO)-ETHANESULFONIC ACID
Molecular weight formula_weight	195.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 11 Entity 11 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	2034

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6. Fold Classification (SCOP + CATH) 15 domains

SCOP 2.08 (6 domains)

Domain ID domain_id	d4upea_
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	d4upeb_
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	d4upec_
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	d4upeq_
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	d4uper_
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	d4upes_
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	4upeA01
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	4upeA02
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	4upeB01
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	4upeB02
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	4upeC01
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	4upeC02
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	4upeQ00
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	4upeR00
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	4upeS00
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	65.430 Å
Unit-cell length b length_b	98.960 Å
Unit-cell length c length_c	184.950 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	91.19 °
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	1.800 Å
Low-resolution limit resolution_low	29.830 Å
R factor r_factor	0.1528
R_work r_work	0.1509
R_free r_free	0.1898

Structure of the unready Ni-A state of the S499C mutant of D. fructosovorans NiFe-hydrogenase

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

NIFE-HYDROGENASE SMALL SUBUNIT

State in the Current Structure

Other States of the Same Protein in the Database

NICKEL-DEPENDENT 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

4upe__assembly_2__model_1

4upe__assembly_2__model_1 | I(q)

4upe__assembly_2__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 (11)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

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 water

6. Fold Classification (SCOP + CATH) 15 domains

SCOP 2.08 (6 domains)

CATH v4.4 (9 domains)

7. Citations (2)

Structure of the unready Ni-A state of the S499C mutant of D. fructosovorans NiFe-hydrogenase

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

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

NICKEL-DEPENDENT 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

4upe__assembly_2__model_1

4upe__assembly_2__model_1 | I(q)

4upe__assembly_2__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 (11)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

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 water

6. Fold Classification (SCOP + CATH) 15 domains

SCOP 2.08 (6 domains)

CATH v4.4 (9 domains)

7. Citations (2)