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9sd6

Crystal structure of the C-terminally truncated human E430Q/E574Q-PGGHG double mutant in complex with kojibiose

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

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9sd6
deposition_date	2025-08-12
last_revision	2026-02-11
title	Crystal structure of the C-terminally truncated human E430Q/E574Q-PGGHG double mutant in complex with kojibiose
keywords	Collagen, glycosylhydrolase, PGGHG, SUGAR BINDING PROTEIN; SUGAR BINDING PROTEIN
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	27.02 Å
rg_electron	26.04 Å
i0	93478100.00
molecular_weight	75932.0 kDa
excluded_volume	94850 Å³
envelope_volume	110350 Å³
shell_volume	34728 Å³
envelope_diameter	99.9 Å
shell_rg	33.86 Å
envelope_rg	26.48 Å
shape_rg	26.04 Å
total_rg	26.81 Å
total_atoms	5364
n_residues	686
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	26.96 Å
rg_real_error	0.88 Å
i0_real	9.3480e+07
i0_real_error	1.4250e+06
rg_reciprocal	26.98 Å
i0_reciprocal	93480000.0000
total_estimate	0.8489
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	32.6 Å
skewness	0.358
kurtosis	-0.147
angular_range	— – 0.2950 Å⁻¹
current_alpha	0.0000
highest_alpha	28150000.0000
n_real_points	60
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.695; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.958; Smooth: 0.990

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4. Crystallography & Experiment

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5. Entities & Polymer Info (6)

Entity 1 polymer

description	Protein-glucosylgalactosylhydroxylysine glucosidase
formula_weight	76075.6 kDa
ec_number	3.2.1.107
mutation	Deletion of the last 45 C-terminal residues (693-737). E430Q and E574Q
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	6066

GMEDAGEDPTTFAAHSLPSDPRLLATVTNAYLGTRVFHDTLHVSGVYNGAGGDTHRAMLPSPLNVRLEAPAGMGEQLTETFALDTNTGSFLHTLEGPRFRASQCIYAHRTLPHVLAFRVSIARLAPGSGPITLLLRSAFSPESPDLDLHQGPDFQGARYLYGHTLTPEQPGGPQQEVHMLWTPAPPDLTLGEGEEARTWDFLTAVGGSQAEAQACLTEALQLQARGALYTAHAQAWAQLWVECGLDVVGPLQLRQALRGSLYYLLSALPQPKAPGYICHGLSPGGLSNGSREECYWGHVFWDQDLWMFPSILMFHPEAARAILEYRIRTLDGALENAQNLGYQGAKFAWESADSGLEVCPEDIYGVQEVHVNGAVVLAFELYYHTTQDLQLFREAGGWDVVRAVAEFWCSRVEWSPREEKYHLRGVMSPDQYHSGVNNSVYTNVLVQNSLRFAAALAQDLGLPIPSQWLAVADKIKVPFDVEQNFHPEFDGYEPGEVVKQADVVLLGYPVPFSLSPDVRRKNLEIYEAVTSPQGPAMTWSMFAVGWMELKDAVRARGLLDRSFANMAEPFKVWTQNADGSGAVNFLTGMGGFLQAVVFGCTGFRVTRAGVTFDPVCLSGISRVSVSGIFYQGNKLNFSFSEDSVTVEVTARAGPWAPHLEAELWPSQSRLSLLPGHKVSFPRSAGRIQMSPPK

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli BL21

Entity 2 branched

description	alpha-D-glucopyranose-(1-2)-alpha-D-glucopyranose
formula_weight	342.3 kDa
src_method	syn
entity_count	1

Entity 3 branched

description	alpha-D-glucopyranose-(1-2)-beta-D-glucopyranose
formula_weight	342.3 kDa
src_method	man
entity_count	1

Entity 4 non-polymer

description	CHLORIDE ION
formula_weight	35.5 kDa
src_method	syn
entity_count	1

Entity 5 non-polymer

description	GLYCEROL
formula_weight	92.1 kDa
src_method	syn
entity_count	3

Entity 6 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	559

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6. Citations (1)

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length_a	54.005 Å
length_b	77.169 Å
length_c	79.055 Å
angle_alpha	90.00 °
angle_beta	99.25 °
angle_gamma	90.00 °
z_pdb	2

space_group	P 1 21 1
int_tables_number	4
crystal_system	—

resolution	1.700 Å
resolution_low	54.928 Å
r_factor	—
r_work	0.1931
r_free	0.2114

fit	/app/data/saxs_computation/sd/9sd6/9sd6.fit
pddf	/app/data/pr_computation/sd/9sd6/9sd6.pr.out
profile	/app/data/saxs_computation/sd/9sd6/9sd6.dat