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9r9s

[FeFe]-hydrogenase from Nitratidesulfovibrio vulgaris str. Hildenborough at pH 5.45

Method: X-RAY DIFFRACTION D_max: 67.6 Å Quality: REASONABLE

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9r9s
deposition_date	2025-05-20
last_revision	2026-06-03
title	[FeFe]-hydrogenase from Nitratidesulfovibrio vulgaris str. Hildenborough at pH 5.45
keywords	[FeFe] hydrogenase, holo hydrogenase, iron-sulfur cluster, metalloenzyme, hydrogen production, OXIDOREDUCTASE; OXIDOREDUCTASE
method	X-RAY DIFFRACTION

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Download Data

SAXS curve (.dat) P(r) distribution (.pr.out) Structure (CIF)

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2. SAXS Parameters (CRYSOL)

rg_guinier	21.83 Å
rg_electron	21.01 Å
i0	52668200.00
molecular_weight	55120.0 kDa
excluded_volume	68149 Å³
envelope_volume	75593 Å³
shell_volume	28336 Å³
envelope_diameter	70.3 Å
shell_rg	29.29 Å
envelope_rg	21.50 Å
shape_rg	21.07 Å
total_rg	21.71 Å
total_atoms	7543
n_residues	484
n_harmonics	20
q_range	— – 0.5000 Å⁻¹
n_points	101
shell_type	directional
solvent_density	0.3340 e/Å³
contrast_shell	0.0300 e/Å³
crysol_version	4.1.3

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3. P(r) Analysis (GNOM)

dmax	67.6 Å
rg_real	21.67 Å
rg_real_error	0.24 Å
i0_real	5.2670e+07
i0_real_error	6.2990e+05
rg_reciprocal	21.70 Å
i0_reciprocal	52670000.0000
total_estimate	0.7166
solution_quality	REASONABLE a REASONABLE solution
n_peaks	2
r_peak_primary	26.2 Å
skewness	0.166
kurtosis	-0.459
angular_range	— – 0.3650 Å⁻¹
current_alpha	0.0000
highest_alpha	17960000.0000
n_real_points	68
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.902; Stabil: 1.000; Sysdev: 0.207; Positv: 1.000; Valcen: 0.990; Smooth: 0.996

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4. Crystallography & Experiment

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5. Entities & Polymer Info (8)

Entity 1 polymer

description	Periplasmic [Fe] hydrogenase large subunit
formula_weight	44397.1 kDa
ec_number	1.12.7.2
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	7879

MSRTVMERIEYEMHTPDPKADPDKLHFVQIDEAKCIGCDTCSQYCPTAAIFGEMGEPHSIPHIEACINCGQCLTHCPENAIYEAQSWVPEVEKKLKDGKVKCIAMPAPAVRYALGDAFGMPVGSVTTGKMLAALQKLGFAHCWDTEFTADVTIWEEGSEFVERLTKKSDMPLPQFTSCCPGWQKYAETYYPELLPHFSTCKSPIGMNGALAKTYGAERMKYDPKQVYTVSIMPCIAKKYEGLRPELKSSGMRDIDATLTTRELAYMIKKAGIDFAKLPDGKRDSLMGESTGGATIFGVTGGVMEAALRFAYEAVTGKKPDSWDFKAVRGLDGIKEATVNVGGTDVKVAVVHGAKRFKQVCDDVKAGKSPYHFIEYMACPGGCVCGGGQPVMPGVLEAWSHPQFEK

Source

organism	Nitratidesulfovibrio vulgaris str. Hildenborough
ncbi_taxonomy_id	882
host_organism	Escherichia coli BL21(DE3)

Entity 2 polymer

description	Periplasmic [Fe] hydrogenase small subunit
formula_weight	10082.4 kDa
ec_number	1.12.7.2
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	B

VKQIKDYMLDRINGVYGADAKFPVRASQDNTQVKALYKSYLEKPLGHKSHDLLHTHWFDKSKGVKELTTAGKLPNPRASEFEGPYPYE

Source

organism	Nitratidesulfovibrio vulgaris str. Hildenborough
ncbi_taxonomy_id	882
host_organism	Escherichia coli BL21(DE3)

Entity 3 non-polymer

description	IRON/SULFUR CLUSTER
formula_weight	351.6 kDa
src_method	syn
entity_count	3

Entity 4 non-polymer

description	dicarbonyl[bis(cyanide-kappaC)]-mu-(iminodimethanethiolatato-1kappaS:2kappaS)-mu-(oxomethylidene)diiron(2+)
formula_weight	355.0 kDa
src_method	syn
entity_count	1

Entity 5 non-polymer

description	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
formula_weight	238.3 kDa
src_method	syn
entity_count	1

Entity 6 non-polymer

description	TRIETHYLENE GLYCOL
formula_weight	150.2 kDa
src_method	syn
entity_count	1

Entity 7 non-polymer

description	DI(HYDROXYETHYL)ETHER
formula_weight	106.1 kDa
src_method	syn
entity_count	1

Entity 8 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	229

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6. Citations (1)

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length_a	49.225 Å
length_b	87.200 Å
length_c	88.732 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	4

space_group	P 21 21 21
int_tables_number	19
crystal_system	—

resolution	1.707 Å
resolution_low	44.405 Å
r_factor	—
r_work	0.1365
r_free	0.1745

fit	/app/data/saxs_computation/r9/9r9s/9r9s.fit
pddf	/app/data/pr_computation/r9/9r9s/9r9s.pr.out
profile	/app/data/saxs_computation/r9/9r9s/9r9s.dat

[FeFe]-hydrogenase from Nitratidesulfovibrio vulgaris str. Hildenborough at pH 5.45

SAXS Profile

P(r) Distribution

1. Structure Basics

Download Data

2. SAXS Parameters (CRYSOL)

3. P(r) Analysis (GNOM)

4. Crystallography & Experiment

Unit Cell

Symmetry

Refinement

Diffraction

5. Entities & Polymer Info (8)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 non-polymer

Entity 4 non-polymer

Entity 5 non-polymer

Entity 6 non-polymer

Entity 7 non-polymer

Entity 8 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)