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9qdc

Nitratidesulfovibrio vulgaris [FeFe]-hydrogenase crystallized in the sodium formate buffer at pH 4.6

Method: X-RAY DIFFRACTION D_max: 67.2 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9qdc
deposition_date	2025-03-06
last_revision	2026-03-18
title	Nitratidesulfovibrio vulgaris [FeFe]-hydrogenase crystallized in the sodium formate buffer at pH 4.6
keywords	[FeFe] 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	21.66 Å
rg_electron	20.86 Å
i0	51105800.00
molecular_weight	54339.0 kDa
excluded_volume	67190 Å³
envelope_volume	73465 Å³
shell_volume	27823 Å³
envelope_diameter	70.9 Å
shell_rg	28.98 Å
envelope_rg	21.32 Å
shape_rg	20.92 Å
total_rg	21.53 Å
total_atoms	7435
n_residues	481
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	67.2 Å
rg_real	21.51 Å
rg_real_error	0.29 Å
i0_real	5.1110e+07
i0_real_error	6.1640e+05
rg_reciprocal	21.54 Å
i0_reciprocal	51110000.0000
total_estimate	0.8960
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	26.1 Å
skewness	0.173
kurtosis	-0.451
angular_range	— – 0.3650 Å⁻¹
current_alpha	0.0000
highest_alpha	17010000.0000
n_real_points	68
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.900; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.991; Smooth: 0.952

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

Entity 1 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
atom_count	8075

VKQIKDYMLDRINGVYGADAKFPVRASQDNTQVKALYKSYLEKPLGHKSHDLLHTHWFDKSKGVKELTTAGKLPNPRASEFEGPYPYE

Source

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

Entity 2 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

MSRTVMERIEYEMHTPDPKADPDKLHFVQIDEAKCIGCDTCSQYCPTAAIFGEMGEPHSIPHIEACINCGQCLTHCPENAIYEAQSWVPEVEKKLKDGKVKCIAMPAPAVRYALGDAFGMPVGSVTTGKMLAALQKLGFAHCWDTEFTADVTIWEEGSEFVERLTKKSDMPLPQFTSCCPGWQKYAETYYPELLPHFSTCKSPIGMNGALAKTYGAERMKYDPKQVYTVSIMPCIAKKYEGLRPELKSSGMRDIDATLTTRELAYMIKKAGIDFAKLPDGKRDSLMGESTGGATIFGVTGGVMEAALRFAYEAVTGKKPDSWDFKAVRGLDGIKEATVNVGGTDVKVAVVHGAKRFKQVCDDVKAGKSPYHFIEYMACPGGCVCGGGQPVMPGVLEAWSHPQFEK

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 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	410

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6. Citations (1)

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length_a	49.535 Å
length_b	87.568 Å
length_c	89.200 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	1.491 Å
resolution_low	44.640 Å
r_factor	—
r_work	0.1473
r_free	0.1815

fit	/app/data/saxs_computation/qd/9qdc/9qdc.fit
pddf	/app/data/pr_computation/qd/9qdc/9qdc.pr.out
profile	/app/data/saxs_computation/qd/9qdc/9qdc.dat

Nitratidesulfovibrio vulgaris [FeFe]-hydrogenase crystallized in the sodium formate buffer at pH 4.6

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 (5)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 non-polymer

Entity 4 non-polymer

Entity 5 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)