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9sw3

Structure of the MvhAGD-HdrABC dimer of M. marburgensis under state 2 substate b (composite structure)

Method: ELECTRON MICROSCOPY D_max: 176.5 Å Quality: REASONABLE

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9sw3
deposition_date	2025-10-04
title	Structure of the MvhAGD-HdrABC dimer of M. marburgensis under state 2 substate b (composite structure)
keywords	Oxidoreductase, hydrogenase, dehydrogenase, polyferredoxin; OXIDOREDUCTASE
method	ELECTRON MICROSCOPY

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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	54.39 Å
rg_electron	55.53 Å
i0	791535000.00
molecular_weight	226690.0 kDa
excluded_volume	280080 Å³
envelope_volume	382260 Å³
shell_volume	62443 Å³
envelope_diameter	187.1 Å
shell_rg	51.01 Å
envelope_rg	54.48 Å
shape_rg	55.66 Å
total_rg	54.97 Å
total_atoms	30648
n_residues	2002
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	176.5 Å
rg_real	54.96 Å
rg_real_error	2.56 Å
i0_real	7.9150e+08
i0_real_error	1.6150e+07
rg_reciprocal	53.90 Å
i0_reciprocal	790300000.0000
total_estimate	0.5430
solution_quality	REASONABLE a REASONABLE solution
n_peaks	2
r_peak_primary	36.5 Å
skewness	0.508
kurtosis	-0.484
angular_range	— – 0.1450 Å⁻¹
current_alpha	0.0000
highest_alpha	36480000.0000
n_real_points	30
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.754; Stabil: 1.000; Sysdev: 0.017; Positv: 1.000; Valcen: 0.729; Smooth: 0.013

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4. Crystallography & Experiment

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5. Entities & Polymer Info (11)

Entity 1 polymer

description	H(2):CoB-CoM heterodisulfide,ferredoxin reductase subunit A
formula_weight	72265.0 kDa
ec_number	1.8.98.5
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	30648

MAEEKKETMEEPKIGVYVCHCGVNIGGVVDVEAVRDYAAKLPNVVIAKDYKYYCSDPGQLEIQKDIKELGINRVVVAACSPRLHEPTFRRCVEEAGLNQFLFEFANIREHDSWVHMDNPEGATEKAKDLVRMAVAKARLLEPLEASKVSVDDKALVIGGGVAGIQAALDLADMGFKTYMVEKRPSISGRMGQLDKTFPTLDCSMCILAPKMVDVGKHDNIELITYAEVKEVDGYIGNFKVKIEKKPRYIDEELCTGCGSCVEVCPIEMPNYFDEGIGMTKAVYIPFPQAVPLCATIDKDYCIECMLCDEVCERGAVKHDQEPEEIEIEVGTIIVATGYDAYDPTEKLEYGYGRHTNVITGLELERMINASGPTDGKVLKPSDGEKPKRVAFIHCVGSRDEQIGKPYCSRVCCMYIMKNAQLIKDKMPDTEVTLYYMDIRAFGKGFEEFYKRSQEKYGIKFIRGRPAEVIENPDLTLTVRSEDTLLGKVTEYDYDMVVLGVGLVPPEGAETLRQTIGLSKSADGFLMEAHPKLRPVDTLTDGVYLAGVAQGPKDIPDAVAQASGAAARAAIPMVKGEVEIEPIIAVTDSDVCGGCEVCIELCPFGAISIEEGHANVNVALCKGCGTCVAACPSGAMDQQHFKTEQIMAQIEAALNEPASK

Entity 2 polymer

description	H(2):CoB-CoM heterodisulfide,ferredoxin reductase subunit B
formula_weight	33496.4 kDa
ec_number	1.8.98.5
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	B

MEIAYFLGCIMNNRYPGIEKATRVLFDKLGIELKDMEGASCCPAPGVFGSFDKTTWAAIAARNITIAEDMGADIMTECNGCFGSLFETNHLLKEDEEMKAKINEILKETGREYKGEVNVRHFAEVLYNDVGLDKLSELVEKPLNLNVAVHYGCHFLKPSDEINIDNPERPTILDEIVEVTGAKSVEYKDKMMCCGAGGGVRSRDLDVALDFTREKLTNMKEAGVDAIVNVCPFCHLQFDVGQMEIKDKFGEEFDIPVLHLAQLLGLAMGLPKEDLVVDAHQVCVDECLEKLEELDRLAPGSG

Entity 3 polymer

description	H(2):CoB-CoM heterodisulfide,ferredoxin reductase subunit C
formula_weight	20548.7 kDa
ec_number	1.8.98.5
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	C

MTLLQREENIIRKGNIDKEFSEKIKAAGGDSLEYCFQCGTCTGSCPSGRRTPYRVRQIIRKANVGLKDEIISDPTLWMCTTCYSCQERCPRKVKIVDVVKLARNEAAKAGFMAPAHKAVGSFVIKTGHGVPINDATMELRKAVGLGELPPTTHQFPEALEEVQKIIKATGFDQLIGYNWETGELE

Entity 4 polymer

description	F420-non-reducing hydrogenase iron-sulfur subunit D
formula_weight	15954.4 kDa
ec_number	1.12.99.-
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	D

MAEDDIKIVMFCCNWCSYGGADTAGTARMQYPTNIRVIRVMCSGRIEPQFVFKAFREGADGVLVTGCHHGDCHYDAGNYKLDRRMRLIYKLADELGIGRERIHHDWISASEGEKFAETVKMMVDRIRALGPSPIKKQLAEA

Entity 5 polymer

description	F420-non-reducing hydrogenase subunit G
formula_weight	33786.6 kDa
ec_number	1.12.99.-
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	E

MAEKIKIGTMWLGGCSGCHLSIADFHEKLLDVMEHADFEFSPVLMDTKYDEIPELDVVVIEGGIVNDENREFAEELREKAKFVISYGTCAVYGGIPGLRNLWDKDEVIEEAYINSITTPNEEGVIPSEDVPHLEGRVKPLGEVIDVDFEVPGCPPRSDVAAEVVMALLKGEEIELPSTNLCEVCPREKPPEGLAMDFIKRQFEVGKPEDDLCLIPQGLICMGPATVSICGAECPSIAIPCRGCYGPTARVEDQGAKMISAIASDYKVEEDKTVDPEEVAEQLDDIVGTFYTFTLPAALIPMKIKKEGK

Entity 6 polymer

description	F420-non-reducing hydrogenase subunit A
formula_weight	52905.1 kDa
ec_number	1.12.99.-
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	F

MVKLTMEPVTRIEGHAKITVHLDDAGNVEDTRLHVMEFRGFEKFLQGRPIEEAPRIVPRICGICDVQHHLAAAKAVDACFGFEPDDVLPAAYKMREIMNWGSYMHSHGLHFYFLAAPDFIAGKDRKTRNVFQIIKDAPDVALQAIELRKNALEIVRATGGRPIHPTSSTPGGISTELDDETQKDLLQKAQRNVELAEATLELAVPIFEENIDLVNSLGNIETYHTGLVKNGVWDVYDGIVRIKDKEGNLFREFKPADYADTIAEHVKPYSWLKFPYIKDLGYPDGVYRVSPLSRLNVADKMPDAAPKAQDYFKEFQDKFGYAQQTLLYHWARLIEVLACAECAADALEGDLSGEKFPDSLERQAGDGVGIVEAPRGTLTHHYTCDENGLITKANIVVATIQNNPAMEMGIQKVAQDYIKPGVEVDDKIFNLMEMVIRAYDPCLSCATHTIDSQMRLATLEVYDSEGDLVKRI

Entity 7 non-polymer

description	IRON/SULFUR CLUSTER
formula_weight	351.6 kDa
src_method	syn
entity_count	11

Entity 8 non-polymer

description	FLAVIN-ADENINE DINUCLEOTIDE
formula_weight	785.5 kDa
src_method	syn
entity_count	1

Entity 9 non-polymer

description	Non-cubane [4Fe-4S]-cluster
formula_weight	351.6 kDa
src_method	syn
entity_count	2

Entity 10 non-polymer

description	FE2/S2 (INORGANIC) CLUSTER
formula_weight	175.8 kDa
src_method	syn
entity_count	1

Entity 11 non-polymer

description	formyl[bis(hydrocyanato-1kappaC)]ironnickel(Fe-Ni)
formula_weight	195.6 kDa
src_method	syn
entity_count	1

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6. Citations (1)

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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	—

space_group	P 1
int_tables_number	1
crystal_system	—

resolution	3.250 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	3.25 Å
resolution_method	—
num_particles	14332

fit	/app/data/saxs_computation/sw/9sw3/9sw3.fit
pddf	/app/data/pr_computation/sw/9sw3/9sw3.pr.out
profile	/app/data/saxs_computation/sw/9sw3/9sw3.dat

Structure of the MvhAGD-HdrABC dimer of M. marburgensis under state 2 substate b (composite structure)

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

EM 3D

5. Entities & Polymer Info (11)

Entity 1 polymer

Polymer

Entity 2 polymer

Polymer

Entity 3 polymer

Polymer

Entity 4 polymer

Polymer

Entity 5 polymer

Polymer

Entity 6 polymer

Polymer

Entity 7 non-polymer

Entity 8 non-polymer

Entity 9 non-polymer

Entity 10 non-polymer

Entity 11 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)