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9rjw

W-formate dehydrogenase from Nitratidesulfovibrio vulgaris (Desulfovibrio vulgaris) - aerobic soaked with 100 bar Kr

Method: X-RAY DIFFRACTION D_max: 96.2 Å Quality: REASONABLE

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9rjw
deposition_date	2025-06-12
title	W-formate dehydrogenase from Nitratidesulfovibrio vulgaris (Desulfovibrio vulgaris) - aerobic soaked with 100 bar Kr
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	30.10 Å
rg_electron	29.54 Å
i0	311115000.00
molecular_weight	136140.0 kDa
excluded_volume	167480 Å³
envelope_volume	191090 Å³
shell_volume	50459 Å³
envelope_diameter	103.7 Å
shell_rg	39.23 Å
envelope_rg	30.08 Å
shape_rg	29.59 Å
total_rg	30.09 Å
total_atoms	9421
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	96.2 Å
rg_real	29.95 Å
rg_real_error	0.48 Å
i0_real	3.1110e+08
i0_real_error	4.4730e+06
rg_reciprocal	30.02 Å
i0_reciprocal	311100000.0000
total_estimate	0.6894
solution_quality	REASONABLE a REASONABLE solution
n_peaks	2
r_peak_primary	36.3 Å
skewness	0.233
kurtosis	-0.356
angular_range	— – 0.2650 Å⁻¹
current_alpha	0.0000
highest_alpha	97160000.0000
n_real_points	54
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.871; Stabil: 1.000; Sysdev: 0.135; Positv: 1.000; Valcen: 0.989; Smooth: 0.952

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4. Crystallography & Experiment

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5. Entities & Polymer Info (11)

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	10014

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	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	4

Entity 8 non-polymer

description	DI(HYDROXYETHYL)ETHER
formula_weight	106.1 kDa
src_method	syn
entity_count	2

Entity 9 non-polymer

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

Entity 10 non-polymer

description	KRYPTON
formula_weight	83.8 kDa
src_method	syn
entity_count	13

Entity 11 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	593

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6. Citations (1)

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length_a	64.665 Å
length_b	128.313 Å
length_c	148.735 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	1.640 Å
resolution_low	97.155 Å
r_factor	—
r_work	0.1877
r_free	0.2187

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

W-formate dehydrogenase from Nitratidesulfovibrio vulgaris (Desulfovibrio vulgaris) - aerobic soaked with 100 bar Kr

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 (11)

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 non-polymer

Entity 10 non-polymer

Entity 11 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)