4u9h

Ultra High Resolution Structure Of The Ni-R State Of [Nife]Hydrogenase From Desulufovibrio Vulgaris Miyazaki F

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 （P21852） IRON/SULFUR CLUSTER × 2 FE3-S4 CLUSTER × 1 (4S)-2-METHYL-2,4-PENTANEDIOL × 12 hydrido[hydridonickel(2+)]bis(hydrocyanato-1kappaC)(hydroxymethyl)iron × 1 MAGNESIUM ION × 1 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PHNS_DESVM
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain S； PDBConstruct 1–265； UniProt 53–317

Periplasmic [NiFe] hydrogenase large subunit

OrganismNot specified

UniProt P21852

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 （P21853） IRON/SULFUR CLUSTER × 2 FE3-S4 CLUSTER × 1 (4S)-2-METHYL-2,4-PENTANEDIOL × 12 hydrido[hydridonickel(2+)]bis(hydrocyanato-1kappaC)(hydroxymethyl)iron × 1 MAGNESIUM ION × 1 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PHNL_DESVM
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain L； PDBConstruct 1–533； UniProt 20–552

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	4u9h
Deposition date deposition_date	2014-08-06
Structure title title	Ultra High Resolution Structure Of The Ni-R State Of [Nife]Hydrogenase From Desulufovibrio Vulgaris Miyazaki F
Keywords keywords	metal-hydride, 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.

4u9h__assembly_1__model_1

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

Download this curve (.dat)

4u9h__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4u9h__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	25.71 Å
Rg (electron density)	24.77 Å
Total Rg	25.62 Å
Atom count	12368
Residues	798
Excluded volume	113000 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4u9h__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 (9)

Entity 1 Entity 1 polymer

Description description	Periplasmic [NiFe] hydrogenase small subunit
Molecular weight formula_weight	28545.4 kDa
EC 编号 ec_number	1.12.2.1
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	S
Atom count atom_count	14147

GPRRPSVVYLHNAECTGCSESVLRAFEPYIDTLILDTLSLDYHETIMAAAGDAAEAALEQAVNSPHGFIAVVEGGIPTAANGIYGKVANHTMLDICSRILPKAQAVIAYGTCATFGGVQAAKPNPTGAKGVNDALKHLGVKAINIAGCPPNPYNLVGTIVYYLKNKAAPELDSLNRPTMFFGQTVHEQCPRLPHFDAGEFAPSFESEEARKGWCLYELGCKGPVTMNNCPKIKFNQTNWPVDAGHPCIGCSEPDFWDAMTPFYQN

Entity 2 Entity 2 polymer

Description description	Periplasmic [NiFe] hydrogenase large subunit
Molecular weight formula_weight	59107.3 kDa
EC 编号 ec_number	1.12.2.1
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	L

SYSGPIVVDPVTRIEGHLRIEVEVENGKVKNAYSSSTLFRGLEIILKGRDPRDAQHFTQRTCGVCTYTHALASTRCVDNAVGVHIPKNATYIRNLVLGAQYLHDHIVHFYHLHALDFVDVTAALKADPAKAAKVASSISPRKTTAADLKAVQDKLKTFVESGQLGPFTNAYFLGGHPAYYLDPETNLIATAHYLEALRLQVKAARAMAVFGAKNPHTQFTVVGGVTCYDALTPQRIAEFEALWKETKAFVDEVYIPDLLVVAAAYKDWTQYGGTDNFITFGEFPKDEYDLNSRFFKPGVVFKRDFKNIKPFDKMQIEEHVRHSWYEGAEARHPWKGQTQPKYTDLHGDDRYSWMKAPRYMGEPMETGPLAQVLIAYSQGHPKVKAVTDAVLAKLGVGPEALFSTLGRTAARGIETAVIAEYVGVMLQEYKDNIAKGDNVICAPWEMPKQAEGVGFVNAPRGGLSHWIRIEDGKIGNFQLVVPSTWTLGPRCDKNKLSPVEASLIGTPVADAKRPVEILRTVHSFDPCIACGVH

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	2

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	1

Entity 5 Entity 5 non-polymer

Description description	(4S)-2-METHYL-2,4-PENTANEDIOL
Molecular weight formula_weight	118.2 kDa
Source method src_method	syn
Copy count entity_count	12

Entity 6 Entity 6 non-polymer

Description description	hydrido[hydridonickel(2+)]bis(hydrocyanato-1kappaC)(hydroxymethyl)iron
Molecular weight formula_weight	198.6 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 7 Entity 7 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 8 Entity 8 non-polymer

Description description	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
Molecular weight formula_weight	122.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 9 Entity 9 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	911

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6. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d4u9hl_
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	d4u9hs_
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

CATH v4.4 (3 domains)

Domain ID domain_id	4u9hL00
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	4u9hS01
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	4u9hS02
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

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Unit-cell length a length_a	66.530 Å
Unit-cell length b length_b	97.950 Å
Unit-cell length c length_c	125.850 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	—

Resolution resolution	0.890 Å
Low-resolution limit resolution_low	37.636 Å
R factor r_factor	0.0960
R_work r_work	0.0955
R_free r_free	0.1063

Ultra High Resolution Structure Of The Ni-R State Of [Nife]Hydrogenase From Desulufovibrio Vulgaris Miyazaki F

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

4u9h__assembly_1__model_1

4u9h__assembly_1__model_1 | I(q)

4u9h__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 (9)

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 water

6. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (2 domains)

CATH v4.4 (3 domains)

7. Citations (1)

Ultra High Resolution Structure Of The Ni-R State Of [Nife]Hydrogenase From Desulufovibrio Vulgaris Miyazaki F

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

4u9h__assembly_1__model_1

4u9h__assembly_1__model_1 | I(q)

4u9h__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 (9)

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 water

6. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (2 domains)

CATH v4.4 (3 domains)

7. Citations (1)