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9rk1

W-formate dehydrogenase W491E from Nitratidesulfovibrio vulgaris (Desulfovibrio vulgaris)

Method: X-RAY DIFFRACTION D_max: 99.3 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9rk1
deposition_date	2025-06-12
title	W-formate dehydrogenase W491E from Nitratidesulfovibrio vulgaris (Desulfovibrio vulgaris)
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	30.32 Å
rg_electron	29.70 Å
i0	298867000.00
molecular_weight	134640.0 kDa
excluded_volume	166480 Å³
envelope_volume	193800 Å³
shell_volume	50938 Å³
envelope_diameter	104.8 Å
shell_rg	39.36 Å
envelope_rg	30.19 Å
shape_rg	29.74 Å
total_rg	30.32 Å
total_atoms	9380
n_residues	1181
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	99.3 Å
rg_real	30.17 Å
rg_real_error	0.62 Å
i0_real	2.9890e+08
i0_real_error	4.2960e+06
rg_reciprocal	30.23 Å
i0_reciprocal	298900000.0000
total_estimate	0.8824
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	38.2 Å
skewness	0.225
kurtosis	-0.361
angular_range	— – 0.2600 Å⁻¹
current_alpha	0.0000
highest_alpha	97400000.0000
n_real_points	53
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.834; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.996; Smooth: 0.968

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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	112379.9 kDa
ec_number	1.2.1.2
mutation	W491E
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	9585

MTVTRRHFLKLSAGAAVAGAFTGLGLSLAPTVARAELQKLQWAKQTTSICCYCAVGCGLIVHTAKDGQGRAVNVEGDPDHPINEGSLCPKGASIFQLGENDQRGTQPLYRAPFSDTWKPVTWDFALTEIAKRIKKTRDASFTEKNAAGDLVNRTEAIASFGSAAMDNEECWAYGNILRSLGLVYIEHQARIUHSPTVPALAESFGRGAMTNHWNDLANSDCILIMGSNAAENHPIAFKWVLRAKDKGATLIHVDPRFTRTSARCDVYAPIRSGADIPFLGGLIKYILDNKLYFTDYVREYTNASLIVGEKFSFKDGLFSGYDAANKKYDKSMWAFELDANGVPKRDPALKHPRCVINLLKKHYERYNLDKVAAITGTSKEQLQQVYKAYAATGKPDKAGTIMYAMGWTQHSVGVQNIRAMAMIQLLLGNIGVAGGGVNALRGESNVQGSTDQGLLAHIWPGYNPVPNSKAATLELYNAATPQSKDPMSVNEWQNRPKYVASYLKALYPDEEPAAAYDYLPRIDAGRKLTDYFWLNIFEKMDKGEFKGLFAWGMNPACGGANANKNRKAMGKLEWLVNVNLFENETSSFWKGPGMNPAEIGTEVFFLPCCVSIEKEGSVANSGRWMQWRYRGPKPYAETKPDGDIMLDMFKKVRELYAKEGGAYPAPIAKLNIADWEEHNEFSPTKVAKLMNGYFLKDTEVGGKQFKKGQQVPSFAFLTADGSTCSGNWLHAGSFTDAGNLMARRDKTQTPEQARIGLFPNWSFCWPVNRRILYNRASVDKTGKPWNPAKAVIEWKDGKWVGDVVDGGGDPGTKHPFIMQTHGFGALYGPGREEGPFPEHYEPLECPVSKNPFSKQLHNPVAFQIEGEKKAVCDPRYPFIGTTYRVTEHWQTGLMTRRCAWLVEAEPQIFCEISKELAKLRGIGNGDTVKVSSLRGALEAVAIVTERIRPFKIEGVDVHMVGLPWHYGWMVPKNGGDTANLLTPSAGDPNTGIPETKAFMVDVRKVWSHPQFEK

Source

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

Entity 2 polymer

description	Formate dehydrogenase, beta subunit, putative
formula_weight	23858.3 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	B

GKMFFVDLSRCTACRGCQIACKQWKNLPAEETRNTGSHQNPPDLSYVTLKTVRFTEKSRKGPGIDWLFFPEQCRHCVEPPCKGQADVDLEGAVVKDETTGAVLFTELTAKVDGESVRSACPYDIPRIDPVTKRLSKCDMCNDRVQNGLLPACVKTCPTGTMNFGDEQEMLALAEKRLAEVKKTYPGAVLGDPNDVRVVYLFTRDPKDFYEHAVA

Source

organism	Nitratidesulfovibrio vulgaris str. Hildenborough
ncbi_taxonomy_id	882
host_organism	Nitratidesulfovibrio 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	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

Entity 7 non-polymer

description	GLYCEROL
formula_weight	92.1 kDa
src_method	syn
entity_count	1

Entity 8 non-polymer

description	1,2-ETHANEDIOL
formula_weight	62.1 kDa
src_method	syn
entity_count	4

Entity 9 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	199

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6. Citations (1)

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length_a	64.824 Å
length_b	128.043 Å
length_c	148.748 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	1.993 Å
resolution_low	74.374 Å
r_factor	—
r_work	0.2086
r_free	0.2582

fit	/app/data/saxs_computation/rk/9rk1/9rk1.fit
pddf	/app/data/pr_computation/rk/9rk1/9rk1.pr.out
profile	/app/data/saxs_computation/rk/9rk1/9rk1.dat

W-formate dehydrogenase W491E from Nitratidesulfovibrio vulgaris (Desulfovibrio vulgaris)

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)