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9ras

Streptococcus pyogenes GapN in complex with imidazoline-2,4-dione

Method: X-RAY DIFFRACTION D_max: 168.1 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9ras
deposition_date	2025-05-21
title	Streptococcus pyogenes GapN in complex with imidazoline-2,4-dione
keywords	GapN, OXIDOREDUCTASE, Soaking, Fragment screening; OXIDOREDUCTASE
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	50.60 Å
rg_electron	50.34 Å
i0	2240430000.00
molecular_weight	407010.0 kDa
excluded_volume	514210 Å³
envelope_volume	651840 Å³
shell_volume	105190 Å³
envelope_diameter	181.0 Å
shell_rg	56.07 Å
envelope_rg	49.61 Å
shape_rg	50.31 Å
total_rg	50.59 Å
total_atoms	57679
n_residues	3799
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	168.1 Å
rg_real	50.59 Å
rg_real_error	1.68 Å
i0_real	2.2400e+09
i0_real_error	4.4810e+07
rg_reciprocal	50.59 Å
i0_reciprocal	2240000000.0000
total_estimate	0.8707
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	59.6 Å
skewness	0.388
kurtosis	-0.220
angular_range	— – 0.1550 Å⁻¹
current_alpha	0.0000
highest_alpha	253200000.0000
n_real_points	32
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.839; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.799

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

Entity 1 polymer

description	NADP-dependent glyceraldehyde-3-phosphate dehydrogenase
formula_weight	52959.2 kDa
src_method	man
entity_count	8

Polymer

type	polypeptide(L)
strand_id	A,B,C,D,E,F,G,H
atom_count	65210

ASWSHPQFEKIEGRRDRGPEFLAKQYKNLVNGEWKLSENEITIYAPATGEELGSVPAMTQAEVDAVYASAKKALSDWRTLSYVERAAYLHKAADILVRDAEKIGAILSKEVAKGHKAAVSEVIRTAEIINYAAEEGLRMEGEVLEGGSFEAASKKKIAIVRREPVGLVLAISPFNYPVNLAGSKIAPALIAGNVVALKPPTQGSISGLLLAEAFAEAGIPAGVFNTITGRGSVIGDYIVEHEAVNFINFTGSTPIGEGIGKLAGMRPIMLELGGKDSAIVLEDADLALAAKNIVAGAFGYSGQRSTAVKRVLVMDKVADQLAAEIKTLVEKLSVGMPEDDADITPLIDTSAADFVEGLIKDATDKGATALTAFNREGNLISPVLFDHVTTDMRLAWEEPFGPVLPIIRVTTVEEAIKISNESEYGLQASIFTTNFPKAFGIAEQLEVGTVHLNNKTQRGTDNFPFLGAKKSGAGVQGVKYSIEAMTTVKSVVFDIQ

Source

organism	Streptococcus pyogenes
ncbi_taxonomy_id	1314
host_organism	Escherichia coli BL21

Entity 2 non-polymer

description	1~{H}-imidazole-2,4-diol
formula_weight	100.1 kDa
src_method	syn
entity_count	21

Entity 3 non-polymer

description	SULFATE ION
formula_weight	96.1 kDa
src_method	syn
entity_count	12

Entity 4 non-polymer

description	GLYCEROL
formula_weight	92.1 kDa
src_method	syn
entity_count	9

Entity 5 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	4556

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6. Citations (1)

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length_a	97.153 Å
length_b	97.154 Å
length_c	100.702 Å
angle_alpha	76.94 °
angle_beta	77.99 °
angle_gamma	68.28 °
z_pdb	8

space_group	P 1
int_tables_number	1
crystal_system	triclinic

resolution	1.570 Å
resolution_low	46.580 Å
r_factor	0.1567
r_work	0.1548
r_free	0.1912

fit	/app/data/saxs_computation/ra/9ras/9ras.fit
pddf	/app/data/pr_computation/ra/9ras/9ras.pr.out
profile	/app/data/saxs_computation/ra/9ras/9ras.dat