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9wxb

Cryo-EM structure of reduced form of formatedehydrogenase from Rhodobacter aestuarii (RaFDH) with NADH

Method: ELECTRON MICROSCOPY D_max: 161.0 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9wxb
deposition_date	2025-09-25
title	Cryo-EM structure of reduced form of formatedehydrogenase from Rhodobacter aestuarii (RaFDH) with NADH
keywords	formate dehydrogenase, formate oxidation, carbon dioxide redcution, FMN, NAD, 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	49.90 Å
rg_electron	50.09 Å
i0	2109060000.00
molecular_weight	364830.0 kDa
excluded_volume	448090 Å³
envelope_volume	562540 Å³
shell_volume	91829 Å³
envelope_diameter	168.5 Å
shell_rg	54.93 Å
envelope_rg	49.76 Å
shape_rg	50.26 Å
total_rg	49.67 Å
total_atoms	25368
n_residues	3324
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	161.0 Å
rg_real	49.70 Å
rg_real_error	1.19 Å
i0_real	2.1090e+09
i0_real_error	3.9350e+07
rg_reciprocal	49.90 Å
i0_reciprocal	2110000000.0000
total_estimate	0.8904
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	70.4 Å
skewness	0.136
kurtosis	-0.620
angular_range	— – 0.1600 Å⁻¹
current_alpha	0.0000
highest_alpha	915100000.0000
n_real_points	33
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.909; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.844

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4. Crystallography & Experiment

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5. Entities & Polymer Info (10)

Entity 1 polymer

description	Formate dehydrogenase delta subunit
formula_weight	7180.2 kDa
ec_number	1.17.1.9
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	G,H
atom_count	25368

MSDEKLIRMANQIAAFFAVQPADRAEGVAAHISDNWAAPMRAALLAHIAAGGAGLDALVVDAAPHIRPAG

Source

organism	Rhodobacter aestuarii
ncbi_taxonomy_id	453582
host_organism	Escherichia coli MC1061

Entity 2 polymer

description	Formate dehydrogenase gamma subunit
formula_weight	19331.0 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	E,F

SRAWRHPQGGSHHHHHHGMRDLYDDDDKHMTDLARLRAILTAHEGREGALLPILHDVQADYGHIPDAALEPIAKALRLSRAEVAGVVGFYHDFRRSPAGKHVIKLCRAEACQAMGGDGVQARLEAALGLKLGETKHDITLEAAYCLGLCACAPAAMVNDALVGRLDDAAVDTIAAEVRA

Source

organism	Rhodobacter aestuarii
ncbi_taxonomy_id	453582
host_organism	Escherichia coli MC1061

Entity 3 polymer

description	Formate dehydrogenase alpha subunit
formula_weight	103751.0 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	B,A

MKDLIIPPLDWTQDMGTPARHGAPVTLTVDGVEVTVPAGTSVLRAAAQAGISIPKLCATDSVEPVGSCRLCMVEIEGMRGMPSSCTTPVAAGMQVHTQTPQLQKLRRGVMELYISDHPLDCLTCAANGDCELQDMAGAVGLREVRYTKGENHFEVRQGGEANPCYIPKDTSNPYFSYDPAKCIVCMRCVRACEEVQGTFALTVDGRGFEARISPAADNFLASDCVSCGACVQACPTATLVEKSVEEIGTPERKVVTTCAYCGVGCSFEAHMRGEELVRMVPWKGGAANRGHSCVKGRFAYGYATHRDRILKPMIREKVSDPWREVSWEEALGFTAARLNAARATHGADALGVITSSRCTNEETYLVQKLARAVFGTNNTDTCARVCHSPTGYGLKQTFGTSAGTQDFDSVEDTDLALVIGANPTDGHPVFASRLRKRLRAGAKLIVVDPRRIDLLETPHIGDSWHLPLRPGTNVAVLVALAHVIVTEKLYDAAFISERCDGDEWADYAEFVSNPEYAPEAVESLTGVPADTLREAARAYAAAPNAAIYYGLGVTEHSQGSTTVIAIANLAMMTGNIGRPGVGVNPLRGQNNVQGSCDMGSFPHELPGYRHVADDAARSLFEKAWGVALSSEPGLRIPNMLDAAVAGQFKALYVQGEDILQSDPDTRHVAAGLAAMDLVIVHDLFLNETANYAHVFLPGSSFLEKDGTFTNAERRINRVRRVMRPKNGYADWEVTQLLANALGAGWAYTHPREIMAEIAATTPGFANVTYEMLDARGSVQWPCNEAAPEGSPIMHVDGFVRGKGRFIRTAYLPTDERTGPRFPLLLTTGRILSQYNVGAQTRRTENVAWHAEDRLEIHPTDAENRGIREGDWVRVASRAGETTLRATVTDRVSPGVVYTTFHHPDTQANVVTTDNSDWATNCPEYKVTAVQVAPSNGPSAWQEDYTAQATAARRIEAA

Source

organism	Rhodobacter aestuarii
ncbi_taxonomy_id	453582
host_organism	Escherichia coli MC1061

Entity 4 polymer

description	Formate dehydrogenase beta subunit
formula_weight	52942.6 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	C,D

MKIWVPCDAAAKACGAERVVAEITAQAAARGVSVDIRRNGTRGMVWLEPLVEVETEAGRVGFGPMTPADVPALFEDLAAHPKALGLVEEIPFFKRQTRLTFARCGRNEPLCLDQYETTGGWDGLRKALAMTPAEVVEEIISSGLRGRGGAGFPTGIKWRTVLGAAADQKYIVCNVDEGDSGSFADRMLIEGDPFCLIEGMAVAGHAVGATRGYVYIRSEYPDCISVMRAAIILAEQSGILAEAGFSLEVRVGAGAYVCGEETAMLNSIEGKRGTVRPKPPLPALEGLFGKPTVVNNLLSLAAVPWILAHGGAAYQSYGIDRSRGTIPLQVGGNVKYGGLFETGFGITLGELVMDVCGGTASGRPVKAVQVGGPLGAYHPQADFDLPFCYELFAGQGGLVGHAGLVVHDDRADMLKLARFAMEFCAVESCGTCTPCRIGAVRGVETLDRIAAGDAAALPLLDDLCDTMKYGSLCALGGFTPYPVQSAIRHFPQDFPVLREAA

Source

organism	Rhodobacter aestuarii
ncbi_taxonomy_id	453582
host_organism	Escherichia coli MC1061

Entity 5 non-polymer

description	FE2/S2 (INORGANIC) CLUSTER
formula_weight	175.8 kDa
src_method	syn
entity_count	4

Entity 6 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	4

Entity 7 non-polymer

description	MOLYBDENUM(VI) ION
formula_weight	95.9 kDa
src_method	syn
entity_count	2

Entity 8 non-polymer

description	IRON/SULFUR CLUSTER
formula_weight	351.6 kDa
src_method	syn
entity_count	10

Entity 9 non-polymer

description	NICOTINAMIDE-ADENINE-DINUCLEOTIDE
formula_weight	663.4 kDa
src_method	syn
entity_count	2

Entity 10 non-polymer

description	FLAVIN MONONUCLEOTIDE
formula_weight	456.3 kDa
src_method	syn
entity_count	2

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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	2.900 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	2.90 Å
resolution_method	—
num_particles	192652

fit	/app/data/saxs_computation/wx/9wxb/9wxb.fit
pddf	/app/data/pr_computation/wx/9wxb/9wxb.pr.out
profile	/app/data/saxs_computation/wx/9wxb/9wxb.dat

Cryo-EM structure of reduced form of formatedehydrogenase from Rhodobacter aestuarii (RaFDH) with NADH

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 (10)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 polymer

Polymer

Source

Entity 4 polymer

Polymer

Source

Entity 5 non-polymer

Entity 6 non-polymer

Entity 7 non-polymer

Entity 8 non-polymer

Entity 9 non-polymer

Entity 10 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)