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9rju

W-formate dehydrogenase from Nitratidesulfovibrio vulgaris (Desulfovibrio vulgaris) - anaerobic soaked with 50 bar CO2 for 1 min

Method: X-RAY DIFFRACTION D_max: 97.6 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9rju
deposition_date	2025-06-12
title	W-formate dehydrogenase from Nitratidesulfovibrio vulgaris (Desulfovibrio vulgaris) - anaerobic soaked with 50 bar CO2 for 1 min
keywords	Formate, CO2, Molybdenum and Tungsten enzymes, DMSO reductase family, ELECTRON TRANSPORT, 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	30.25 Å
rg_electron	29.66 Å
i0	306038000.00
molecular_weight	135630.0 kDa
excluded_volume	167360 Å³
envelope_volume	193580 Å³
shell_volume	50879 Å³
envelope_diameter	104.9 Å
shell_rg	39.39 Å
envelope_rg	30.21 Å
shape_rg	29.70 Å
total_rg	30.28 Å
total_atoms	9449
n_residues	1182
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	97.6 Å
rg_real	30.10 Å
rg_real_error	0.56 Å
i0_real	3.0600e+08
i0_real_error	4.3930e+06
rg_reciprocal	30.16 Å
i0_reciprocal	306100000.0000
total_estimate	0.8882
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	37.5 Å
skewness	0.230
kurtosis	-0.356
angular_range	— – 0.2600 Å⁻¹
current_alpha	0.0000
highest_alpha	100000000.0000
n_real_points	53
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.856; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.994; Smooth: 0.981

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4. Crystallography & Experiment

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5. Entities & Polymer Info (9)

Entity 1 polymer

description	Formate dehydrogenase, alpha subunit, selenocysteine-containing
formula_weight	112437.0 kDa
ec_number	1.2.1.2
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	9590

MTVTRRHFLKLSAGAAVAGAFTGLGLSLAPTVARAELQKLQWAKQTTSICCYCAVGCGLIVHTAKDGQGRAVNVEGDPDHPINEGSLCPKGASIFQLGENDQRGTQPLYRAPFSDTWKPVTWDFALTEIAKRIKKTRDASFTEKNAAGDLVNRTEAIASFGSAAMDNEECWAYGNILRSLGLVYIEHQARIUHSPTVPALAESFGRGAMTNHWNDLANSDCILIMGSNAAENHPIAFKWVLRAKDKGATLIHVDPRFTRTSARCDVYAPIRSGADIPFLGGLIKYILDNKLYFTDYVREYTNASLIVGEKFSFKDGLFSGYDAANKKYDKSMWAFELDANGVPKRDPALKHPRCVINLLKKHYERYNLDKVAAITGTSKEQLQQVYKAYAATGKPDKAGTIMYAMGWTQHSVGVQNIRAMAMIQLLLGNIGVAGGGVNALRGESNVQGSTDQGLLAHIWPGYNPVPNSKAATLELYNAATPQSKDPMSVNWWQNRPKYVASYLKALYPDEEPAAAYDYLPRIDAGRKLTDYFWLNIFEKMDKGEFKGLFAWGMNPACGGANANKNRKAMGKLEWLVNVNLFENETSSFWKGPGMNPAEIGTEVFFLPCCVSIEKEGSVANSGRWMQWRYRGPKPYAETKPDGDIMLDMFKKVRELYAKEGGAYPAPIAKLNIADWEEHNEFSPTKVAKLMNGYFLKDTEVGGKQFKKGQQVPSFAFLTADGSTCSGNWLHAGSFTDAGNLMARRDKTQTPEQARIGLFPNWSFCWPVNRRILYNRASVDKTGKPWNPAKAVIEWKDGKWVGDVVDGGGDPGTKHPFIMQTHGFGALYGPGREEGPFPEHYEPLECPVSKNPFSKQLHNPVAFQIEGEKKAVCDPRYPFIGTTYRVTEHWQTGLMTRRCAWLVEAEPQIFCEISKELAKLRGIGNGDTVKVSSLRGALEAVAIVTERIRPFKIEGVDVHMVGLPWHYGWMVPKNGGDTANLLTPSAGDPNTGIPETKAFMVDVRKVWSHPQFEK

Source

organism	Nitratidesulfovibrio vulgaris str. Hildenborough
ncbi_taxonomy_id	882
host_organism	Desulfovibrio vulgaris str. Hildenborough

Entity 2 polymer

description	Formate dehydrogenase, beta subunit, putative
formula_weight	23989.5 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	B

MGKMFFVDLSRCTACRGCQIACKQWKNLPAEETRNTGSHQNPPDLSYVTLKTVRFTEKSRKGPGIDWLFFPEQCRHCVEPPCKGQADVDLEGAVVKDETTGAVLFTELTAKVDGESVRSACPYDIPRIDPVTKRLSKCDMCNDRVQNGLLPACVKTCPTGTMNFGDEQEMLALAEKRLAEVKKTYPGAVLGDPNDVRVVYLFTRDPKDFYEHAVA

Source

organism	Nitratidesulfovibrio vulgaris str. Hildenborough
ncbi_taxonomy_id	882
host_organism	Desulfovibrio vulgaris str. Hildenborough

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	4

Entity 5 non-polymer

description	TUNGSTEN ION
formula_weight	183.8 kDa
src_method	syn
entity_count	1

Entity 6 non-polymer

description	HYDROSULFURIC ACID
formula_weight	34.1 kDa
src_method	syn
entity_count	1

Entity 7 non-polymer

description	GLYCEROL
formula_weight	92.1 kDa
src_method	syn
entity_count	4

Entity 8 non-polymer

description	CARBON DIOXIDE
formula_weight	44.0 kDa
src_method	syn
entity_count	18

Entity 9 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	141

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6. Citations (1)

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length_a	65.027 Å
length_b	128.724 Å
length_c	149.861 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	4

space_group	P 21 21 21
int_tables_number	19
crystal_system	—

resolution	2.069 Å
resolution_low	59.653 Å
r_factor	—
r_work	0.2110
r_free	0.2549

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

W-formate dehydrogenase from Nitratidesulfovibrio vulgaris (Desulfovibrio vulgaris) - anaerobic soaked with 50 bar CO2 for 1 min

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

Diffraction

5. Entities & Polymer Info (9)

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

Entity 7 non-polymer

Entity 8 non-polymer

Entity 9 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)