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9qsi

Crystal Structure of Mycobacterium smegmatis thioredoxin reductase in complex with Z166687084

Method: X-RAY DIFFRACTION D_max: 70.4 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9qsi
deposition_date	2025-04-04
last_revision	2026-04-15
title	Crystal Structure of Mycobacterium smegmatis thioredoxin reductase in complex with Z166687084
keywords	TrxR, Oxidoreductase, Fragment; 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	21.65 Å
rg_electron	21.09 Å
i0	40405400.00
molecular_weight	31927.0 kDa
excluded_volume	30326 Å³
envelope_volume	50938 Å³
shell_volume	20589 Å³
envelope_diameter	71.3 Å
shell_rg	27.17 Å
envelope_rg	21.20 Å
shape_rg	21.13 Å
total_rg	21.61 Å
total_atoms	2411
n_residues	305
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	70.4 Å
rg_real	21.66 Å
rg_real_error	0.44 Å
i0_real	4.0410e+07
i0_real_error	5.2770e+05
rg_reciprocal	21.66 Å
i0_reciprocal	40410000.0000
total_estimate	0.8902
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	23.1 Å
skewness	0.355
kurtosis	-0.471
angular_range	— – 0.3650 Å⁻¹
current_alpha	0.0000
highest_alpha	9104000.0000
n_real_points	68
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.874; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.961; Smooth: 0.986

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4. Crystallography & Experiment

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5. Entities & Polymer Info (8)

Entity 1 polymer

description	Thioredoxin reductase
formula_weight	34578.7 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	B
atom_count	2636

MAHHHHHHMSTSQTVHDVIIIGSGPAGYTAAIYAARAQLKPLVFEGTQFGGALMTTTEVENYPGFREGITGPELMDQMREQALRFGADLRMEDVDAVQLEGPVKTVVVGDETHQARAVILAMGAAARHLGVPGEEALTGMGVSTCATCDGFFFRDQDIVVVGGGDSAMEEATFLTRFARSVTLIHRRDEFRASKIMLERARANEKITFLTNTEITQIEGDPKVTGVRLRDTVTGEESKLDVTGVFVAIGHDPRSELVRGQVELDDEGYVKVQGRTTYTSLDGVFAAGDLVDHTYRQAITAAGSGCAASIDAERWLAEQD

Source

organism	Mycolicibacterium smegmatis MC2 155
ncbi_taxonomy_id	246196
host_organism	Escherichia coli BL21(DE3)

Entity 2 non-polymer

description	FLAVIN-ADENINE DINUCLEOTIDE
formula_weight	785.5 kDa
src_method	syn
entity_count	1

Entity 3 non-polymer

description	GLYCEROL
formula_weight	92.1 kDa
src_method	syn
entity_count	1

Entity 4 non-polymer

description	MALONATE ION
formula_weight	102.0 kDa
src_method	syn
entity_count	2

Entity 5 non-polymer

description	MAGNESIUM ION
formula_weight	24.3 kDa
src_method	syn
entity_count	1

Entity 6 non-polymer

description	DIMETHYL SULFOXIDE
formula_weight	78.1 kDa
src_method	syn
entity_count	2

Entity 7 non-polymer

description	1-(3-chlorophenyl)urea
formula_weight	170.6 kDa
src_method	syn
entity_count	1

Entity 8 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	188

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6. Citations (1)

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length_a	67.770 Å
length_b	67.770 Å
length_c	155.130 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	120.00 °
z_pdb	6

space_group	P 31 2 1
int_tables_number	152
crystal_system	trigonal

resolution	1.760 Å
resolution_low	46.800 Å
r_factor	0.2096
r_work	0.2084
r_free	0.2336

fit	/app/data/saxs_computation/qs/9qsi/9qsi.fit
pddf	/app/data/pr_computation/qs/9qsi/9qsi.pr.out
profile	/app/data/saxs_computation/qs/9qsi/9qsi.dat