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9rjo

[FeFe]-hydrogenase CpI from Clostridium pasteurianum, variant N160L-Q195L

Method: X-RAY DIFFRACTION D_max: 103.0 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9rjo
deposition_date	2025-06-12
title	[FeFe]-hydrogenase CpI from Clostridium pasteurianum, variant N160L-Q195L
keywords	[FeFe]-hydrogenase I from Clostridium pasteurianum, variant N160L-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	32.21 Å
rg_electron	31.86 Å
i0	298520000.00
molecular_weight	132210.0 kDa
excluded_volume	162400 Å³
envelope_volume	197060 Å³
shell_volume	50079 Å³
envelope_diameter	107.1 Å
shell_rg	39.95 Å
envelope_rg	31.80 Å
shape_rg	32.03 Å
total_rg	31.91 Å
total_atoms	9074
n_residues	1152
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	103.0 Å
rg_real	32.12 Å
rg_real_error	0.59 Å
i0_real	2.9850e+08
i0_real_error	4.5940e+06
rg_reciprocal	32.16 Å
i0_reciprocal	298500000.0000
total_estimate	0.8869
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	39.9 Å
skewness	0.299
kurtosis	-0.338
angular_range	— – 0.2450 Å⁻¹
current_alpha	0.0000
highest_alpha	79880000.0000
n_real_points	50
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.904; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.814

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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	65095.5 kDa
ec_number	1.12.7.2
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	9893

MKTIIINGVQFNTDEDTTILKFARDNNIDISALCFLNNCNNDINKCEICTVEVEGTGLVTACDTLIEDGMIINTNSDAVNEKIKSRISQLLDIHEFKCGPCNRRENCEFLKLVIKYKARASKPFLPKDKTEYVDERSKSLTVDRTKCLLCGRCVNACGKLTETYAMKFLNKNGKTIIGAEDEKCFDDTNCLLCGLCIIACPVAALSEKSHMDRVKNALNAPEKHVIVAMAPSVRASIGELFNMGFGVDVTGKIYTALRQLGFDKIFDINFGADMTIMEEATELVQRIENNGPFPMFTSCCPGWVRQAENYYPELLNNLSSAKSPQQIFGTASKTYYPSISGLDPKNVFTVTVMPCTSKKFEADRPQMEKDGLRDIDAVITTRELAKMIKDAKIPFAKLEDSEADPAMGEYSGAGAIFGATGGVMEAALRSAKDFAENAELEDIEYKQVRGLNGIKEAEVEINNNKYNVAVINGASNLFKFMKSGMINEKQYHFIEVMACHGGCVNGGGQPHVNPKDLEKVDIKKVRASVLYNQDEHLSKRKSHENTALVKMYQNYFGKPGEGRAHEILHFKYKKSAWSHPQFEK

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	MAGNESIUM ION
formula_weight	24.3 kDa
src_method	nat
entity_count	4

Entity 6 non-polymer

description	GLYCEROL
formula_weight	92.1 kDa
src_method	syn
entity_count	2

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	758

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6. Citations (1)

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length_a	89.150 Å
length_b	71.620 Å
length_c	102.500 Å
angle_alpha	90.00 °
angle_beta	97.67 °
angle_gamma	90.00 °
z_pdb	4

space_group	P 1 21 1
int_tables_number	4
crystal_system	—

resolution	1.670 Å
resolution_low	39.190 Å
r_factor	0.1796
r_work	0.1782
r_free	0.2059

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