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9rj9

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

Method: X-RAY DIFFRACTION D_max: 102.5 Å Quality: REASONABLE

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9rj9
deposition_date	2025-06-12
title	[FeFe]-hydrogenase CpI from Clostridium pasteurianum, variant N160L
keywords	[FeFe]-hydrogenase I from Clostridium pasteurianum, variant N160L, 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	32.24 Å
rg_electron	31.91 Å
i0	302867000.00
molecular_weight	133000.0 kDa
excluded_volume	163280 Å³
envelope_volume	198850 Å³
shell_volume	50416 Å³
envelope_diameter	107.9 Å
shell_rg	40.07 Å
envelope_rg	31.83 Å
shape_rg	32.08 Å
total_rg	31.96 Å
total_atoms	9124
n_residues	1156
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	102.5 Å
rg_real	32.15 Å
rg_real_error	0.65 Å
i0_real	3.0290e+08
i0_real_error	4.7560e+06
rg_reciprocal	32.19 Å
i0_reciprocal	302900000.0000
total_estimate	0.6792
solution_quality	REASONABLE a REASONABLE solution
n_peaks	1
r_peak_primary	39.7 Å
skewness	0.298
kurtosis	-0.338
angular_range	— – 0.2450 Å⁻¹
current_alpha	0.0000
highest_alpha	83510000.0000
n_real_points	50
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.911; Stabil: 1.000; Sysdev: 0.096; Positv: 1.000; Valcen: 0.998; Smooth: 0.807

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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	65110.5 kDa
ec_number	1.12.7.2
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	10179

MKTIIINGVQFNTDEDTTILKFARDNNIDISALCFLNNCNNDINKCEICTVEVEGTGLVTACDTLIEDGMIINTNSDAVNEKIKSRISQLLDIHEFKCGPCNRRENCEFLKLVIKYKARASKPFLPKDKTEYVDERSKSLTVDRTKCLLCGRCVNACGKLTETYAMKFLNKNGKTIIGAEDEKCFDDTNCLLCGQCIIACPVAALSEKSHMDRVKNALNAPEKHVIVAMAPSVRASIGELFNMGFGVDVTGKIYTALRQLGFDKIFDINFGADMTIMEEATELVQRIENNGPFPMFTSCCPGWVRQAENYYPELLNNLSSAKSPQQIFGTASKTYYPSISGLDPKNVFTVTVMPCTSKKFEADRPQMEKDGLRDIDAVITTRELAKMIKDAKIPFAKLEDSEADPAMGEYSGAGAIFGATGGVMEAALRSAKDFAENAELEDIEYKQVRGLNGIKEAEVEINNNKYNVAVINGASNLFKFMKSGMINEKQYHFIEVMACHGGCVNGGGQPHVNPKDLEKVDIKKVRASVLYNQDEHLSKRKSHENTALVKMYQNYFGKPGEGRAHEILHFKYKKSAWSHPQFEK

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	syn
entity_count	5

Entity 6 non-polymer

description	GLYCEROL
formula_weight	92.1 kDa
src_method	syn
entity_count	4

Entity 7 non-polymer

description	CHLORIDE ION
formula_weight	35.5 kDa
src_method	syn
entity_count	4

Entity 8 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	921

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6. Citations (1)

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length_a	89.660 Å
length_b	72.280 Å
length_c	102.990 Å
angle_alpha	90.00 °
angle_beta	97.43 °
angle_gamma	90.00 °
z_pdb	4

space_group	P 1 21 1
int_tables_number	4
crystal_system	—

resolution	1.450 Å
resolution_low	38.960 Å
r_factor	0.1699
r_work	0.1688
r_free	0.1908

fit	/app/data/saxs_computation/rj/9rj9/9rj9.fit
pddf	/app/data/pr_computation/rj/9rj9/9rj9.pr.out
profile	/app/data/saxs_computation/rj/9rj9/9rj9.dat