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9rjq

[FeFe]-hydrogenase CpI from Clostridium pasteurianum, variant Q195L

Method: X-RAY DIFFRACTION D_max: 103.2 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9rjq
deposition_date	2025-06-12
title	[FeFe]-hydrogenase CpI from Clostridium pasteurianum, variant Q195L
keywords	[FeFe]-hydrogenase I from Clostridium pasteurianum, variant Q195L, 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	32.30 Å
rg_electron	32.00 Å
i0	296838000.00
molecular_weight	131690.0 kDa
excluded_volume	161690 Å³
envelope_volume	195760 Å³
shell_volume	49627 Å³
envelope_diameter	108.1 Å
shell_rg	39.95 Å
envelope_rg	31.96 Å
shape_rg	32.17 Å
total_rg	32.04 Å
total_atoms	9034
n_residues	1146
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	103.2 Å
rg_real	32.23 Å
rg_real_error	0.72 Å
i0_real	2.9680e+08
i0_real_error	4.7720e+06
rg_reciprocal	32.26 Å
i0_reciprocal	296800000.0000
total_estimate	0.8833
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	40.0 Å
skewness	0.308
kurtosis	-0.339
angular_range	— – 0.2450 Å⁻¹
current_alpha	0.0000
highest_alpha	85430000.0000
n_real_points	50
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.906; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.762

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4. Crystallography & Experiment

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5. Entities & Polymer Info (8)

Entity 1 polymer

description	Iron hydrogenase 1
formula_weight	65096.4 kDa
ec_number	1.12.7.2
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	9956

MKTIIINGVQFNTDEDTTILKFARDNNIDISALCFLNNCNNDINKCEICTVEVEGTGLVTACDTLIEDGMIINTNSDAVNEKIKSRISQLLDIHEFKCGPCNRRENCEFLKLVIKYKARASKPFLPKDKTEYVDERSKSLTVDRTKCLLCGRCVNACGKNTETYAMKFLNKNGKTIIGAEDEKCFDDTNCLLCGLCIIACPVAALSEKSHMDRVKNALNAPEKHVIVAMAPSVRASIGELFNMGFGVDVTGKIYTALRQLGFDKIFDINFGADMTIMEEATELVQRIENNGPFPMFTSCCPGWVRQAENYYPELLNNLSSAKSPQQIFGTASKTYYPSISGLDPKNVFTVTVMPCTSKKFEADRPQMEKDGLRDIDAVITTRELAKMIKDAKIPFAKLEDSEADPAMGEYSGAGAIFGATGGVMEAALRSAKDFAENAELEDIEYKQVRGLNGIKEAEVEINNNKYNVAVINGASNLFKFMKSGMINEKQYHFIEVMACHGGCVNGGGQPHVNPKDLEKVDIKKVRASVLYNQDEHLSKRKSHENTALVKMYQNYFGKPGEGRAHEILHFKYKKSAWSHPQFEK

Source

organism	Clostridium pasteurianum
ncbi_taxonomy_id	1501
host_organism	Escherichia coli BL21(DE3)

Entity 2 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	2

Entity 3 non-polymer

description	IRON/SULFUR CLUSTER
formula_weight	351.6 kDa
src_method	syn
entity_count	8

Entity 4 non-polymer

description	FE2/S2 (INORGANIC) CLUSTER
formula_weight	175.8 kDa
src_method	syn
entity_count	2

Entity 5 non-polymer

description	GLYCEROL
formula_weight	92.1 kDa
src_method	nat
entity_count	3

Entity 6 non-polymer

description	MAGNESIUM ION
formula_weight	24.3 kDa
src_method	syn
entity_count	6

Entity 7 non-polymer

description	CHLORIDE ION
formula_weight	35.5 kDa
src_method	syn
entity_count	2

Entity 8 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	861

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6. Citations (1)

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length_a	87.790 Å
length_b	71.380 Å
length_c	103.250 Å
angle_alpha	90.00 °
angle_beta	101.97 °
angle_gamma	90.00 °
z_pdb	4

space_group	P 1 21 1
int_tables_number	4
crystal_system	—

resolution	1.750 Å
resolution_low	48.110 Å
r_factor	0.1801
r_work	0.1780
r_free	0.2203

fit	/app/data/saxs_computation/rj/9rjq/9rjq.fit
pddf	/app/data/pr_computation/rj/9rjq/9rjq.pr.out
profile	/app/data/saxs_computation/rj/9rjq/9rjq.dat