SAXSdb — 9sd4

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1. Structure Basics

entry_id	9sd4
deposition_date	2025-08-12
last_revision	2026-02-11
title	Human PGGHG crystal structure
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	27.11 Å
rg_electron	26.15 Å
i0	91213800.00
molecular_weight	75030.0 kDa
excluded_volume	93743 Å³
envelope_volume	110660 Å³
shell_volume	34766 Å³
envelope_diameter	99.8 Å
shell_rg	33.88 Å
envelope_rg	26.52 Å
shape_rg	26.15 Å
total_rg	26.92 Å
total_atoms	5303
n_residues	683
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	96.3 Å
rg_real	27.06 Å
rg_real_error	0.73 Å
i0_real	9.1210e+07
i0_real_error	1.5110e+06
rg_reciprocal	27.08 Å
i0_reciprocal	91210000.0000
total_estimate	0.8491
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	32.6 Å
skewness	0.359
kurtosis	-0.144
angular_range	— – 0.2950 Å⁻¹
current_alpha	0.0000
highest_alpha	27570000.0000
n_real_points	60
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.699; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.958; Smooth: 0.977

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4. Crystallography & Experiment

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5. Entities & Polymer Info (3)

Entity 1 polymer

description	Protein-glucosylgalactosylhydroxylysine glucosidase
formula_weight	80783.7 kDa
ec_number	3.2.1.107
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	5388

GMEDAGEDPTTFAAHSLPSDPRLLATVTNAYLGTRVFHDTLHVSGVYNGAGGDTHRAMLPSPLNVRLEAPAGMGEQLTETFALDTNTGSFLHTLEGPRFRASQCIYAHRTLPHVLAFRVSIARLAPGSGPITLLLRSAFSPESPDLDLHQGPDFQGARYLYGHTLTPEQPGGPQQEVHMLWTPAPPDLTLGEGEEARTWDFLTAVGGSQAEAQACLTEALQLQARGALYTAHAQAWAQLWVECGLDVVGPLQLRQALRGSLYYLLSALPQPKAPGYICHGLSPGGLSNGSREECYWGHVFWDQDLWMFPSILMFHPEAARAILEYRIRTLDGALENAQNLGYQGAKFAWESADSGLEVCPEDIYGVQEVHVNGAVVLAFELYYHTTQDLQLFREAGGWDVVRAVAEFWCSRVEWSPREEKYHLRGVMSPDEYHSGVNNSVYTNVLVQNSLRFAAALAQDLGLPIPSQWLAVADKIKVPFDVEQNFHPEFDGYEPGEVVKQADVVLLGYPVPFSLSPDVRRKNLEIYEAVTSPQGPAMTWSMFAVGWMELKDAVRARGLLDRSFANMAEPFKVWTENADGSGAVNFLTGMGGFLQAVVFGCTGFRVTRAGVTFDPVCLSGISRVSVSGIFYQGNKLNFSFSEDSVTVEVTARAGPWAPHLEAELWPSQSRLSLLPGHKVSFPRSAGRIQMSPPKLPGSSSSEFPGRTFSDVRDPLQSPLWVTLGSSSPTESLTVDPASE

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	1

Entity 3 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	37

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6. Citations (1)

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length_a	54.446 Å
length_b	77.302 Å
length_c	80.054 Å
angle_alpha	90.00 °
angle_beta	98.94 °
angle_gamma	90.00 °
z_pdb	2

space_group	P 1 21 1
int_tables_number	4
crystal_system	—

resolution	2.390 Å
resolution_low	55.340 Å
r_factor	0.2436
r_work	0.2411
r_free	0.2930

fit	/app/data/saxs_computation/sd/9sd4/9sd4.fit
pddf	/app/data/pr_computation/sd/9sd4/9sd4.pr.out
profile	/app/data/saxs_computation/sd/9sd4/9sd4.dat

Human PGGHG crystal structure

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