9gz4

FeFe Hydrogenase from Desulfovibrio desulfuricans labelled with cyanophenylalanine - reduced state

Method: X-RAY DIFFRACTION

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

Periplasmic [Fe] hydrogenase large subunit

Desulfovibrio desulfuricans

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Periplasmic [Fe] hydrogenase small subunit × 1 （P07603） IRON/SULFUR CLUSTER × 3 bis(cyanido-kappaC)(dicarbonyl)-mu-(oxomethylidene)[mu-propane-1,3-bis(thiolate)-1kappa~2~S~1~,S~3~:2kappa~2~S~1~,S~3~] diiron(2+) × 1 CHLORIDE ION × 3 LITHIUM ION × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PHFL_NITV2
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–396； UniProt 2–397

Periplasmic [Fe] hydrogenase small subunit

Desulfovibrio desulfuricans

UniProt P07603

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Periplasmic [Fe] hydrogenase large subunit × 1 （P07598） IRON/SULFUR CLUSTER × 3 bis(cyanido-kappaC)(dicarbonyl)-mu-(oxomethylidene)[mu-propane-1,3-bis(thiolate)-1kappa~2~S~1~,S~3~:2kappa~2~S~1~,S~3~] diiron(2+) × 1 CHLORIDE ION × 3 LITHIUM ION × 1 water × 2	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	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–88； UniProt 36–123

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	9gz4
Deposition date deposition_date	2024-10-03
Structure title title	FeFe Hydrogenase from Desulfovibrio desulfuricans labelled with cyanophenylalanine - reduced state
Keywords keywords	Metalloprotein Iron-sulfur cluster 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.

9gz4__assembly_1__model_1

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

Download this curve (.dat)

9gz4__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9gz4__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	21.74 Å
Rg (electron density)	20.91 Å
Total Rg	21.61 Å
Atom count	7404
Residues	480
Excluded volume	67320 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9gz4__assembly_1__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 (7)

Entity 1 Entity 1 polymer

Description description	Periplasmic [Fe] hydrogenase large subunit
Molecular weight formula_weight	43248.8 kDa
EC 编号 ec_number	1.12.7.2
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	8078

SRTVMERIEYEMHTPDPKADPDKLHFVQIDEAKCIGCDTCSQYCPTAAIFGEMGEPHSIPHIEACINCGQCLTHCPENAIYEAQSWVPEVEKKLKDGKVKCIAMPAPAVRYALGDAFGMPVGSVTTGKMLAALQKLGFAHCWDTEFTADVTIWEEGSEFVERLTKKSDMPLPQFTSCCPGWQKYAETYYPELLPHFSTCKSPIGMNGALAKTYGAERMKYDPKQVYTVSIMPCIAKKYEGLRPELKSSGMRDIDATLTTRELAYMIKKAGIDFAKLPDGKRDSLMGESTGGATIFGVTGGVMEAALRFAYEAVTGKKPDSWDFKAVRGLDGIKEATVNVGGTDVKVAVVHGAKRFKQVCDDVKAGKSPYHFIEYMACPGGCVCGGGQPVMPGVLEA

Source Source

Source organism organism	Desulfovibrio desulfuricans
NCBI taxonomy ID ncbi_taxonomy_id	876
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Periplasmic [Fe] hydrogenase small subunit
Molecular weight formula_weight	10082.4 kDa
EC 编号 ec_number	1.12.7.2
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

VKQIKDYMLDRINGVYGADAKFPVRASQDNTQVKALYKSYLEKPLGHKSHDLLHTHWFDKSKGVKELTTAGKLPNPRASEFEGPYPYE

Source Source

Source organism organism	Desulfovibrio desulfuricans
NCBI taxonomy ID ncbi_taxonomy_id	876
Host organism host_organism	Escherichia coli

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	3

Entity 4 Entity 4 non-polymer

Description description	bis(cyanido-kappaC)(dicarbonyl)-mu-(oxomethylidene)[mu-propane-1,3-bis(thiolate)-1kappa~2~S~1~,S~3~:2kappa~2~S~1~,S~3~] diiron(2+)
Molecular weight formula_weight	354.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 6 Entity 6 non-polymer

Description description	LITHIUM ION
Molecular weight formula_weight	6.9 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 7 Entity 7 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	526

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Unit-cell length a length_a	49.718 Å
Unit-cell length b length_b	87.713 Å
Unit-cell length c length_c	89.885 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	4

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	orthorhombic

Resolution resolution	0.960 Å
Low-resolution limit resolution_low	44.940 Å
R factor r_factor	0.1441
R_work r_work	0.1436
R_free r_free	0.1522

FeFe Hydrogenase from Desulfovibrio desulfuricans labelled with cyanophenylalanine - reduced state

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

Periplasmic [Fe] hydrogenase large subunit

State in the Current Structure

Other States of the Same Protein in the Database

Periplasmic [Fe] hydrogenase small 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

9gz4__assembly_1__model_1

9gz4__assembly_1__model_1 | I(q)

9gz4__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 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 water

7. Citations (1)

FeFe Hydrogenase from Desulfovibrio desulfuricans labelled with cyanophenylalanine - reduced state

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

Periplasmic [Fe] 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

Periplasmic [Fe] 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

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

9gz4__assembly_1__model_1

9gz4__assembly_1__model_1 | I(q)

9gz4__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 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 water

7. Citations (1)