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9r4o

Crystal structure of inactive (D163N) variant CtGH76 from Chaetomium thermophilum in complex with alpha-1,6-mannobiose

Method: X-RAY DIFFRACTION D_max: 69.2 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9r4o
deposition_date	2025-05-07
title	Crystal structure of inactive (D163N) variant CtGH76 from Chaetomium thermophilum in complex with alpha-1,6-mannobiose
keywords	Glycoside Hydrolases, carbohydrate-binding protein, HYDROLASE; HYDROLASE
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	20.67 Å
rg_electron	19.40 Å
i0	29472100.00
molecular_weight	40530.0 kDa
excluded_volume	50007 Å³
envelope_volume	55874 Å³
shell_volume	23256 Å³
envelope_diameter	74.4 Å
shell_rg	26.86 Å
envelope_rg	19.88 Å
shape_rg	19.40 Å
total_rg	20.28 Å
total_atoms	2853
n_residues	362
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	69.2 Å
rg_real	20.53 Å
rg_real_error	0.42 Å
i0_real	2.9470e+07
i0_real_error	3.8000e+05
rg_reciprocal	20.55 Å
i0_reciprocal	29470000.0000
total_estimate	0.7852
solution_quality	GOOD a GOOD solution
n_peaks	3
r_peak_primary	27.1 Å
skewness	0.146
kurtosis	-0.326
angular_range	— – 0.3850 Å⁻¹
current_alpha	0.0000
highest_alpha	9155000.0000
n_real_points	70
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.736; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.000

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

Entity 1 polymer

description	Uncharacterized protein
formula_weight	48088.1 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	2925

MAGIADLTAALASADRNRVTRVEAMRRSPTTISLSTLGALSALWGILYFMTCSGRNSRGVLADASSGMLQTRQSDSESLNSTGLAQAAINGLNARFYESSNARWSSDEPWWISGVALTMVIEYMRRSGSKEYLDQVEDVIEVQRQPLSWWPSGEGEFRADATNDTGWWALAMVRMYDLTGNEDYLNISIKDEAYMRQWWTDTECGGGLYVDIQDLTYKNAIANELYLKLVASLANRAPNATIYLDRAQQAWTWFLGSGMINGVNLINDGLARDSNTGSCYNNRLPVWTYNQGVILGALVELYHATKDESYLLSAQAIADAVLSPSNGLTSSSGVLTETCEGSDSCNQDQQVFKGVFALNLAELGDAVAGASSDPDAGQDYREYLDTNMQSMYANDRSEIVPTLFDSSTGDLYDVSWSGPFRNATMPKQASAIGLYVANI

Source

organism	Thermochaetoides thermophila DSM 1495
ncbi_taxonomy_id	759272
host_organism	Escherichia coli B

Entity 2 branched

description	alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose
formula_weight	342.3 kDa
src_method	man
entity_count	1

Entity 3 non-polymer

description	alpha-D-mannopyranose
formula_weight	180.2 kDa
src_method	syn
entity_count	1

Entity 4 non-polymer

description	GLYCEROL
formula_weight	92.1 kDa
src_method	syn
entity_count	1

Entity 5 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	63

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6. Citations (1)

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length_a	107.024 Å
length_b	107.024 Å
length_c	127.541 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	2.130 Å
resolution_low	49.340 Å
r_factor	0.2081
r_work	0.2072
r_free	0.2259

fit	/app/data/saxs_computation/r4/9r4o/9r4o.fit
pddf	/app/data/pr_computation/r4/9r4o/9r4o.pr.out
profile	/app/data/saxs_computation/r4/9r4o/9r4o.dat