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1e9v

XENON BOUND IN HYDROPHOBIC CHANNEL OF HYBRID CLUSTER PROTEIN FROM DESULFOVIBRIO VULGARIS

Method: X-RAY DIFFRACTION D_max: 82.9 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	1e9v
deposition_date	2000-10-27
title	XENON BOUND IN HYDROPHOBIC CHANNEL OF HYBRID CLUSTER PROTEIN FROM DESULFOVIBRIO VULGARIS
keywords	OXIDOREDUCTASE, CUBANE, IRON SULFUR, THIOCYSTEINE, PRISMANE, HYDROPHOBIC CAVITY, S-MERCAPTOCYSTEINE, FUSCOREDOXIN; 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	23.74 Å
rg_electron	23.14 Å
i0	68213000.00
molecular_weight	62732.0 kDa
excluded_volume	77079 Å³
envelope_volume	87177 Å³
shell_volume	30412 Å³
envelope_diameter	82.5 Å
shell_rg	31.18 Å
envelope_rg	23.62 Å
shape_rg	23.27 Å
total_rg	23.55 Å
total_atoms	4270
n_residues	552
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	82.9 Å
rg_real	23.65 Å
rg_real_error	0.62 Å
i0_real	6.8210e+07
i0_real_error	9.4830e+05
rg_reciprocal	23.67 Å
i0_reciprocal	68210000.0000
total_estimate	0.7690
solution_quality	GOOD a GOOD solution
n_peaks	3
r_peak_primary	29.8 Å
skewness	0.294
kurtosis	-0.292
angular_range	— – 0.3350 Å⁻¹
current_alpha	0.0000
highest_alpha	18690000.0000
n_real_points	65
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.681; Stabil: 0.988; Sysdev: 1.000; Positv: 1.000; Valcen: 0.986; Smooth: 0.000

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4. Crystallography & Experiment

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5. Entities & Polymer Info (9)

Entity 1 polymer

description	HYDROXYLAMINE REDUCTASE
formula_weight	60074.7 kDa
ec_number	1.7.-.-
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	5026

MFCFQCQETAKNTGCTVKGMCGKPEETANLQDLLIFVLRGIAIYGEKLKELGQPDRSNDDFVLQGLFATITNANWDDARFEAMISEGLARRDKLRNAFLAVYKAKNGKDFSEPLPEAATWTGDSTAFAEKAKSVGILATENEDVRSLRELLIIGLKGVAAYAEHAAVLGFRKTEIDEFMLEALASTTKDLSVDEMVALVMKAGGMAVTTMALLDEANTTTYGNPEITQVNIGVGKNPGILISGHDLKDMAELLKQTEGTGVDVYTHGEMLPANYYPAFKKYPHFVGNYGGSWWQQNPEFESFNGPILLTTNCLVPLKKENTYLDRLYTTGVVGYEGAKHIADRPAGGAKDFSALIAQAKKCPPPVEIETGSIVGGFAHHQVLALADKVVEAVKSGAIKRFVVMAGCDGRQKSRSYYTEVAENLPKDTVILTAGCAKYRYNKLNLGDIGGIPRVLDAGQCNDSYSLAVIALKLKEVFGLDDINDLPVSYDIAWYEQKAVAVLLALLFLGVKGIRLGPTLPAFLSPNVAKVLVENFNIKPIGTVQDDIAAMMAGK

Source

organism	DESULFOVIBRIO VULGARIS
ncbi_taxonomy_id	881
host_organism	DESULFOVIBRIO VULGARIS

Entity 2 non-polymer

description	IRON/SULFUR/OXYGEN HYBRID CLUSTER
formula_weight	367.6 kDa
src_method	syn
entity_count	1

Entity 3 non-polymer

description	IRON/SULFUR CLUSTER
formula_weight	351.6 kDa
src_method	syn
entity_count	1

Entity 4 non-polymer

description	XENON
formula_weight	131.3 kDa
src_method	syn
entity_count	13

Entity 5 non-polymer

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

Entity 6 non-polymer

description	ACETIC ACID
formula_weight	60.1 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	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
formula_weight	122.1 kDa
src_method	syn
entity_count	1

Entity 9 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	748

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6. Citations (1)

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length_a	63.620 Å
length_b	64.598 Å
length_c	152.254 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	1.790 Å
resolution_low	38.070 Å
r_factor	—
r_work	0.1610
r_free	0.1970

fit	/app/data/saxs_computation/e9/1e9v/1e9v.fit
pddf	/app/data/pr_computation/e9/1e9v/1e9v.pr.out
profile	/app/data/saxs_computation/e9/1e9v/1e9v.dat