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9r4p

Crystal structure of inactive (D164N) variant CtGH76 from Chaetomium thermophilum in complex with alpha-1,6-mannobiose

Method: X-RAY DIFFRACTION D_max: 68.4 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9r4p
deposition_date	2025-05-07
title	Crystal structure of inactive (D164N) 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	20.64 Å
rg_electron	19.38 Å
i0	29611100.00
molecular_weight	40618.0 kDa
excluded_volume	50105 Å³
envelope_volume	55594 Å³
shell_volume	23186 Å³
envelope_diameter	75.5 Å
shell_rg	26.86 Å
envelope_rg	19.84 Å
shape_rg	19.38 Å
total_rg	20.26 Å
total_atoms	2859
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	68.4 Å
rg_real	20.50 Å
rg_real_error	0.36 Å
i0_real	2.9610e+07
i0_real_error	3.3880e+05
rg_reciprocal	20.53 Å
i0_reciprocal	29610000.0000
total_estimate	0.7876
solution_quality	GOOD a GOOD solution
n_peaks	3
r_peak_primary	26.8 Å
skewness	0.143
kurtosis	-0.333
angular_range	— – 0.3850 Å⁻¹
current_alpha	0.0000
highest_alpha	9103000.0000
n_real_points	70
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.747; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.997; Smooth: 0.000

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	CtGH76
formula_weight	48088.1 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	2895

MAGIADLTAALASADRNRVTRVEAMRRSPTTISLSTLGALSALWGILYFMTCSGRNSRGVLADASSGMLQTRQSDSESLNSTGLAQAAINGLNARFYESSNARWSSDEPWWISGVALTMVIEYMRRSGSKEYLDQVEDVIEVQRQPLSWWPSGEGEFRADATDNTGWWALAMVRMYDLTGNEDYLNISIKDEAYMRQWWTDTECGGGLYVDIQDLTYKNAIANELYLKLVASLANRAPNATIYLDRAQQAWTWFLGSGMINGVNLINDGLARDSNTGSCYNNRLPVWTYNQGVILGALVELYHATKDESYLLSAQAIADAVLSPSNGLTSSSGVLTETCEGSDSCNQDQQVFKGVFALNLAELGDAVAGASSDPDAGQDYREYLDTNMQSMYANDRSEIVPTLFDSSTGDLYDVSWSGPFRNATMPKQASAIGLYVANI

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	2

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	36

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6. Citations (1)

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length_a	107.090 Å
length_b	107.090 Å
length_c	127.267 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	2.460 Å
resolution_low	49.350 Å
r_factor	0.2022
r_work	0.2013
r_free	0.2200

fit	/app/data/saxs_computation/r4/9r4p/9r4p.fit
pddf	/app/data/pr_computation/r4/9r4p/9r4p.pr.out
profile	/app/data/saxs_computation/r4/9r4p/9r4p.dat

Crystal structure of inactive (D164N) variant CtGH76 from Chaetomium thermophilum in complex with alpha-1,6-mannobiose

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