SAXSdb — 9vap

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1. Structure Basics

entry_id	9vap
deposition_date	2025-06-03
title	Cryo-EM structure of formate dehydrogenase from Shewanella oneidensis MR-1 (SoFdhAB)
keywords	Formate dehydrogenase, carbon dioxide reduction, tungsten (W)-dependent, OXIDOREDUCTASE; 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	30.10 Å
rg_electron	29.31 Å
i0	259201000.00
molecular_weight	121900.0 kDa
excluded_volume	149340 Å³
envelope_volume	181570 Å³
shell_volume	48897 Å³
envelope_diameter	102.2 Å
shell_rg	38.57 Å
envelope_rg	29.55 Å
shape_rg	29.28 Å
total_rg	30.13 Å
total_atoms	8459
n_residues	1063
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	93.3 Å
rg_real	29.95 Å
rg_real_error	0.49 Å
i0_real	2.5920e+08
i0_real_error	3.4800e+06
rg_reciprocal	30.01 Å
i0_reciprocal	259200000.0000
total_estimate	0.8973
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	37.0 Å
skewness	0.203
kurtosis	-0.402
angular_range	— – 0.2650 Å⁻¹
current_alpha	0.0000
highest_alpha	64800000.0000
n_real_points	54
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.914; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.984; Smooth: 0.934

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4. Crystallography & Experiment

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5. Entities & Polymer Info (6)

Entity 1 polymer

description	Formate dehydrogenase molybdopterin-binding subunit FdhA
formula_weight	105996.2 kDa
ec_number	1.1.5.6
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	8459

MRLTRKTDPVVEPKVPALGLNRRQFLKSAGLATGGIAAASMLGTGMMRKAEAKDIPHNAPTEVKRTICSHCSVGCGVYAEVQNGVWTGQEPAFDHPFNQGGHCAKGAALREHGHGEKRLKYPMKLEGGKWKKISWDQAINEVGDKMMAIRQESGPDSIYFMGSAKFSNEQAYLYRKFAALWGTNNVDHSARICHSTTVAGVANTWGYGAQTNSVNDIRHSKCILFVGSNPSEAHPVAMQHILVAKERGAKIIVVDPRFTRTAAKSDEYVHIRPGTDIPFIYGLLWHIFENGWEDKDFIKRRVYGMERIREEVKKYTPEEVENVVGAPKAQMYRVAKMMAETKPGSIVWCMGGTQHHVGNANTRSYCILQLALGNMGVTGGGTNIFRGHDNVQGASDFGLSFDDLPGYFGLTSGSWAHWANVWDLDPKWVTSRFDQGEYLGQSPQTSPGIPCSRWHDGVLEDKTKIAQKDNIRLAFFWGQSVNTETRGREVRQALDKMDTVVVVDPFPTMAGVMHQRKDGVYLLPAATQFETYGSVSATNRSIQWRSKVIEPLFESLPDHVIMCKLAKKVGIDKELFKHIKVNGEEPLIEDIVREYNRGMWTIGYTGQSPERLKMHQENWGTFNVDSLEAPGGPAKGETYGLPWPCWGTPEMKHPGSHILYNETKHVKDGGGSFRARFGVERNGVNLLSEEAYSAGSEIQDGYPEFTADMLKQLGWWDDLTEDEKKYAEGKNWKTDISGGIQRVVIKHGCIPYGNGKARAVVWNFPDDIPLHREPLYTPRRDLVAKYPTYEDRMVARLPTLYKSIQDKDFAKDFPLALTSGRLVEYEGGGEETRSNPWLAELQQEMFIEISPADAADRGIRDGDNVFVHSPEGAKITVKAMVTPRVVPGECFMPYHFAGVFEGESLAKNYPEGTVPYVIGESANTILTYGYDVVTQMQETKSSLCQISKA

Source

organism	Shewanella oneidensis MR-1
ncbi_taxonomy_id	211586
host_organism	Shewanella oneidensis MR-1

Entity 2 polymer

description	4Fe-4S dicluster domain-containing protein
formula_weight	22411.7 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	B

MAVMKFLCDTKRCIECNGCVTACKNENDSALEWGIQRRRVVTINDGQPGEASISVACMHCTDAPCMAVCPADCFYRTDDGIVLHNKDTCIGCGYCFYACPFGAPQFPKKTAFGSRGKMDKCTFCAGGPEETFSEAEHKKYGANRIAEGKLPMCAELCATKALLAGDAEVVSNIYRQRMASRGNPNVIWGYNPKTGEINHHHHHH

Source

organism	Shewanella oneidensis MR-1
ncbi_taxonomy_id	211586
host_organism	Shewanella oneidensis MR-1

Entity 3 non-polymer

description	2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,7,8A,9-TETRAHYDRO-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-4-ONE GUANOSINE DINUCLEOTIDE
formula_weight	740.6 kDa
src_method	syn
entity_count	2

Entity 4 non-polymer

description	IRON/SULFUR CLUSTER
formula_weight	351.6 kDa
src_method	syn
entity_count	5

Entity 5 non-polymer

description	HYDROSULFURIC ACID
formula_weight	34.1 kDa
src_method	syn
entity_count	1

Entity 6 non-polymer

description	TUNGSTEN ION
formula_weight	183.8 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	2.75 Å
resolution_method	—
num_particles	138699

fit	/app/data/saxs_computation/va/9vap/9vap.fit
pddf	/app/data/pr_computation/va/9vap/9vap.pr.out
profile	/app/data/saxs_computation/va/9vap/9vap.dat

Cryo-EM structure of formate dehydrogenase from Shewanella oneidensis MR-1 (SoFdhAB)

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

EM 3D

5. Entities & Polymer Info (6)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 non-polymer

Entity 4 non-polymer

Entity 5 non-polymer

Entity 6 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)