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9sd8

Crystal structure of C-terminally truncated human PGGHG in complex with glucose.

Method: X-RAY DIFFRACTION D_max: 114.6 Å Quality: EXCELLENT

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9sd8
deposition_date	2025-08-12
last_revision	2026-02-11
title	Crystal structure of C-terminally truncated human PGGHG in complex with glucose.
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	36.05 Å
rg_electron	35.32 Å
i0	346752000.00
molecular_weight	151210.0 kDa
excluded_volume	188920 Å³
envelope_volume	232350 Å³
shell_volume	52731 Å³
envelope_diameter	119.5 Å
shell_rg	43.34 Å
envelope_rg	35.20 Å
shape_rg	35.33 Å
total_rg	35.82 Å
total_atoms	10681
n_residues	1364
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	114.6 Å
rg_real	35.92 Å
rg_real_error	0.91 Å
i0_real	3.4680e+08
i0_real_error	5.6440e+06
rg_reciprocal	36.00 Å
i0_reciprocal	346800000.0000
total_estimate	0.9050
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	1
r_peak_primary	44.3 Å
skewness	0.177
kurtosis	-0.577
angular_range	— – 0.2200 Å⁻¹
current_alpha	0.0000
highest_alpha	58110000.0000
n_real_points	45
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.939; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.945

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4. Crystallography & Experiment

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5. Entities & Polymer Info (7)

Entity 1 polymer

description	Protein-glucosylgalactosylhydroxylysine glucosidase
formula_weight	76077.6 kDa
ec_number	3.2.1.107
mutation	Deletion of the last 45 C-terminal residues (693-737)
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	11700

GMEDAGEDPTTFAAHSLPSDPRLLATVTNAYLGTRVFHDTLHVSGVYNGAGGDTHRAMLPSPLNVRLEAPAGMGEQLTETFALDTNTGSFLHTLEGPRFRASQCIYAHRTLPHVLAFRVSIARLAPGSGPITLLLRSAFSPESPDLDLHQGPDFQGARYLYGHTLTPEQPGGPQQEVHMLWTPAPPDLTLGEGEEARTWDFLTAVGGSQAEAQACLTEALQLQARGALYTAHAQAWAQLWVECGLDVVGPLQLRQALRGSLYYLLSALPQPKAPGYICHGLSPGGLSNGSREECYWGHVFWDQDLWMFPSILMFHPEAARAILEYRIRTLDGALENAQNLGYQGAKFAWESADSGLEVCPEDIYGVQEVHVNGAVVLAFELYYHTTQDLQLFREAGGWDVVRAVAEFWCSRVEWSPREEKYHLRGVMSPDEYHSGVNNSVYTNVLVQNSLRFAAALAQDLGLPIPSQWLAVADKIKVPFDVEQNFHPEFDGYEPGEVVKQADVVLLGYPVPFSLSPDVRRKNLEIYEAVTSPQGPAMTWSMFAVGWMELKDAVRARGLLDRSFANMAEPFKVWTENADGSGAVNFLTGMGGFLQAVVFGCTGFRVTRAGVTFDPVCLSGISRVSVSGIFYQGNKLNFSFSEDSVTVEVTARAGPWAPHLEAELWPSQSRLSLLPGHKVSFPRSAGRIQMSPPK

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli BL21

Entity 2 non-polymer

description	CHLORIDE ION
formula_weight	35.5 kDa
src_method	syn
entity_count	3

Entity 3 non-polymer

description	alpha-D-glucopyranose
formula_weight	180.2 kDa
src_method	nat
entity_count	2

Entity 4 non-polymer

description	beta-D-glucopyranose
formula_weight	180.2 kDa
src_method	syn
entity_count	3

Entity 5 non-polymer

description	GLYCEROL
formula_weight	92.1 kDa
src_method	syn
entity_count	4

Entity 6 non-polymer

description	DI(HYDROXYETHYL)ETHER
formula_weight	106.1 kDa
src_method	syn
entity_count	1

Entity 7 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	794

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6. Citations (1)

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length_a	55.323 Å
length_b	75.891 Å
length_c	318.908 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	8

space_group	P 21 21 21
int_tables_number	19
crystal_system	—

resolution	1.610 Å
resolution_low	159.450 Å
r_factor	0.1756
r_work	0.1738
r_free	0.2094

fit	/app/data/saxs_computation/sd/9sd8/9sd8.fit
pddf	/app/data/pr_computation/sd/9sd8/9sd8.pr.out
profile	/app/data/saxs_computation/sd/9sd8/9sd8.dat