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1e08

Structural model of the [Fe]-Hydrogenase/cytochrome c553 complex combining NMR and soft-docking

D_max: 80.6 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	1e08
deposition_date	2000-03-13
title	Structural model of the [Fe]-Hydrogenase/cytochrome c553 complex combining NMR and soft-docking
keywords	HYDROGENASE, CYTOCHROME C553, ELECTRON TRANSFER COMPLEX; HYDROGENASE

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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	23.19 Å
rg_electron	22.60 Å
i0	62785900.00
molecular_weight	60558.0 kDa
excluded_volume	74935 Å³
envelope_volume	81317 Å³
shell_volume	29118 Å³
envelope_diameter	80.9 Å
shell_rg	30.66 Å
envelope_rg	23.08 Å
shape_rg	22.69 Å
total_rg	23.14 Å
total_atoms	5055
n_residues	537
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	80.6 Å
rg_real	23.12 Å
rg_real_error	0.56 Å
i0_real	6.2790e+07
i0_real_error	8.6720e+05
rg_reciprocal	23.14 Å
i0_reciprocal	62790000.0000
total_estimate	0.8621
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	27.3 Å
skewness	0.314
kurtosis	-0.260
angular_range	— – 0.3400 Å⁻¹
current_alpha	0.0000
highest_alpha	18750000.0000
n_real_points	66
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.744; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.990; Smooth: 0.982

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4. Crystallography & Experiment

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5. Entities & Polymer Info (11)

Entity 1 polymer

description	[FE]-HYDROGENASE (LARGE SUBUNIT)
formula_weight	40239.4 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	5058

FVQIDEAKCIGCDTCSQYCPTAAIFGEMGEPHSIPHIEACINCGQCLTHCPENAIYEAQSWVPEVEKKLKDGKVKCIAMPAPAVRYALGDAFGMPVGSVTTGKMLAALQKLGFAHCWDTEFTADVTIWEEGSEFVERLTKKSDMPLPQFTSCCPGWQKYAETYYPELLPHFSTCKSPIGMNGALAKTYGAERMKYDPKQVYTVSIMPCIAKKYEGLRPELKSSGMRDIDATLTTRELAYMIKKAGIDFAKLPDGKRDSLMGESTGGATIFGVTGGVMEAALRFAYEAVTGKKPDSWDFKAVRGLDGIKEATVNVGGTDVKVAVVHGAKRFKQVCDDVKAGKSPYHFIEYMACPGGCVCGGGQPVMPGVLEA

Entity 2 polymer

description	[FE]-HYDROGENASE (SMALL SUBUNIT)
formula_weight	10082.4 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	D

VKQIKDYMLDRINGVYGADAKFPVRASQDNTQVKALYKSYLEKPLGHKSHDLLHTHWFDKSKGVKELTTAGKLPNPRASEFEGPYPYE

Entity 3 polymer

description	CYTOCHROME C553
formula_weight	8246.5 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	E

DGAALYKSCIGCHGADGSKAAMGSAKPVKGQGAEELYKKMKGYADGSYGGERKAMMTNAVKKYSDEELKALADYMSKL

Entity 4 non-polymer

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

Entity 5 non-polymer

description	1,3-PROPANEDITHIOL
formula_weight	108.2 kDa
src_method	syn
entity_count	1

Entity 6 non-polymer

description	FE (II) ION
formula_weight	55.8 kDa
src_method	syn
entity_count	2

Entity 7 non-polymer

description	CYANIDE ION
formula_weight	26.0 kDa
src_method	syn
entity_count	2

Entity 8 non-polymer

description	CARBON MONOXIDE
formula_weight	28.0 kDa
src_method	syn
entity_count	2

Entity 9 non-polymer

description	ZINC ION
formula_weight	65.4 kDa
src_method	syn
entity_count	1

Entity 10 non-polymer

description	HEME C
formula_weight	618.5 kDa
src_method	syn
entity_count	1

Entity 11 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	1

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6. Citations (2)

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length_a	1.000 Å
length_b	1.000 Å
length_c	1.000 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	1

space_group	P 1
int_tables_number	1
crystal_system	—

fit	/app/data/saxs_computation/e0/1e08/1e08.fit
pddf	/app/data/pr_computation/e0/1e08/1e08.pr.out
profile	/app/data/saxs_computation/e0/1e08/1e08.dat

Structural model of the [Fe]-Hydrogenase/cytochrome c553 complex combining NMR and soft-docking

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

5. Entities & Polymer Info (11)

Entity 1 polymer

Polymer

Entity 2 polymer

Polymer

Entity 3 polymer

Polymer

Entity 4 non-polymer

Entity 5 non-polymer

Entity 6 non-polymer

Entity 7 non-polymer

Entity 8 non-polymer

Entity 9 non-polymer

Entity 10 non-polymer

Entity 11 water

6. Citations (2)

7. Files & Curves (10)

Files (7)

Curves (3)