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9sd7

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

Method: X-RAY DIFFRACTION D_max: 97.7 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9sd7
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	27.03 Å
rg_electron	26.08 Å
i0	93659800.00
molecular_weight	75989.0 kDa
excluded_volume	94899 Å³
envelope_volume	110020 Å³
shell_volume	34667 Å³
envelope_diameter	99.7 Å
shell_rg	33.79 Å
envelope_rg	26.44 Å
shape_rg	26.09 Å
total_rg	26.83 Å
total_atoms	5366
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	97.7 Å
rg_real	26.98 Å
rg_real_error	0.80 Å
i0_real	9.3660e+07
i0_real_error	1.3250e+06
rg_reciprocal	26.99 Å
i0_reciprocal	93660000.0000
total_estimate	0.8409
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	33.1 Å
skewness	0.359
kurtosis	-0.146
angular_range	— – 0.2950 Å⁻¹
current_alpha	0.0000
highest_alpha	29070000.0000
n_real_points	60
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.662; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.941; Smooth: 0.999

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

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	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	6287

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	2

Entity 3 non-polymer

description	GLYCEROL
formula_weight	92.1 kDa
src_method	syn
entity_count	5

Entity 4 non-polymer

description	beta-D-glucopyranose
formula_weight	180.2 kDa
src_method	syn
entity_count	1

Entity 5 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	694

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6. Citations (1)

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length_a	54.021 Å
length_b	77.382 Å
length_c	78.814 Å
angle_alpha	90.00 °
angle_beta	99.68 °
angle_gamma	90.00 °
z_pdb	2

space_group	P 1 21 1
int_tables_number	4
crystal_system	—

resolution	1.390 Å
resolution_low	77.690 Å
r_factor	0.1535
r_work	0.1520
r_free	0.1800

fit	/app/data/saxs_computation/sd/9sd7/9sd7.fit
pddf	/app/data/pr_computation/sd/9sd7/9sd7.pr.out
profile	/app/data/saxs_computation/sd/9sd7/9sd7.dat