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9rav

Streptococcus pyogenes GapN in complex with 4-hydroxypyridazine

Method: X-RAY DIFFRACTION D_max: 170.0 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9rav
deposition_date	2025-05-21
title	Streptococcus pyogenes GapN in complex with 4-hydroxypyridazine
keywords	GapN, OXIDOREDUCTASE, Fragment screening, Soaking; 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	50.73 Å
rg_electron	50.49 Å
i0	2197330000.00
molecular_weight	404740.0 kDa
excluded_volume	511980 Å³
envelope_volume	642480 Å³
shell_volume	103580 Å³
envelope_diameter	184.2 Å
shell_rg	55.97 Å
envelope_rg	49.75 Å
shape_rg	50.46 Å
total_rg	50.74 Å
total_atoms	57415
n_residues	3795
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	170.0 Å
rg_real	50.74 Å
rg_real_error	1.80 Å
i0_real	2.1970e+09
i0_real_error	4.6710e+07
rg_reciprocal	50.72 Å
i0_reciprocal	2197000000.0000
total_estimate	0.8702
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	60.3 Å
skewness	0.394
kurtosis	-0.227
angular_range	— – 0.1550 Å⁻¹
current_alpha	0.0000
highest_alpha	246500000.0000
n_real_points	32
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.828; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.827

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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	62655

ASWSHPQFEKIEGRRDRGPEFLAKQYKNLVNGEWKLSENEITIYAPATGEELGSVPAMTQAEVDAVYASAKKALSDWRTLSYVERAAYLHKAADILVRDAEKIGAILSKEVAKGHKAAVSEVIRTAEIINYAAEEGLRMEGEVLEGGSFEAASKKKIAIVRREPVGLVLAISPFNYPVNLAGSKIAPALIAGNVVALKPPTQGSISGLLLAEAFAEAGIPAGVFNTITGRGSVIGDYIVEHEAVNFINFTGSTPIGEGIGKLAGMRPIMLELGGKDSAIVLEDADLALAAKNIVAGAFGYSGQRSTAVKRVLVMDKVADQLAAEIKTLVEKLSVGMPEDDADITPLIDTSAADFVEGLIKDATDKGATALTAFNREGNLISPVLFDHVTTDMRLAWEEPFGPVLPIIRVTTVEEAIKISNESEYGLQASIFTTNFPKAFGIAEQLEVGTVHLNNKTQRGTDNFPFLGAKKSGAGVQGVKYSIEAMTTVKSVVFDIQ

Source

organism	Streptococcus pyogenes
ncbi_taxonomy_id	1314
host_organism	Escherichia coli BL21

Entity 2 non-polymer

description	SULFATE ION
formula_weight	96.1 kDa
src_method	syn
entity_count	13

Entity 3 non-polymer

description	4-hydroxypyridazine
formula_weight	96.1 kDa
src_method	syn
entity_count	8

Entity 4 non-polymer

description	GLYCEROL
formula_weight	92.1 kDa
src_method	syn
entity_count	3

Entity 5 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	4462

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6. Citations (1)

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length_a	97.574 Å
length_b	98.985 Å
length_c	103.231 Å
angle_alpha	77.68 °
angle_beta	75.95 °
angle_gamma	67.51 °
z_pdb	8

space_group	P 1
int_tables_number	1
crystal_system	triclinic

resolution	1.500 Å
resolution_low	48.420 Å
r_factor	0.1698
r_work	0.1679
r_free	0.2066

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