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9rau

Streptococcus pyogenes GapN in complex with pyrimidine-5-amine

Method: X-RAY DIFFRACTION D_max: 168.3 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9rau
deposition_date	2025-05-21
title	Streptococcus pyogenes GapN in complex with pyrimidine-5-amine
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	50.67 Å
rg_electron	50.43 Å
i0	2261720000.00
molecular_weight	407790.0 kDa
excluded_volume	514920 Å³
envelope_volume	650710 Å³
shell_volume	104770 Å³
envelope_diameter	182.9 Å
shell_rg	56.08 Å
envelope_rg	49.77 Å
shape_rg	50.41 Å
total_rg	50.65 Å
total_atoms	57857
n_residues	3796
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	168.3 Å
rg_real	50.66 Å
rg_real_error	1.59 Å
i0_real	2.2620e+09
i0_real_error	4.5620e+07
rg_reciprocal	50.66 Å
i0_reciprocal	2262000000.0000
total_estimate	0.8712
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	59.7 Å
skewness	0.387
kurtosis	-0.227
angular_range	— – 0.1550 Å⁻¹
current_alpha	0.0000
highest_alpha	249700000.0000
n_real_points	32
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.840; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.801

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4. Crystallography & Experiment

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5. Entities & Polymer Info (8)

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	61356

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	16

Entity 3 non-polymer

description	pyrimidin-5-amine
formula_weight	95.1 kDa
src_method	syn
entity_count	8

Entity 4 non-polymer

description	2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
formula_weight	209.2 kDa
src_method	syn
entity_count	8

Entity 5 non-polymer

description	GLYCEROL
formula_weight	92.1 kDa
src_method	syn
entity_count	8

Entity 6 non-polymer

description	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
formula_weight	238.3 kDa
src_method	syn
entity_count	2

Entity 7 non-polymer

description	CHLORIDE ION
formula_weight	35.5 kDa
src_method	syn
entity_count	1

Entity 8 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	2920

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6. Citations (1)

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length_a	97.764 Å
length_b	98.946 Å
length_c	103.032 Å
angle_alpha	78.04 °
angle_beta	75.63 °
angle_gamma	67.01 °
z_pdb	8

space_group	P 1
int_tables_number	1
crystal_system	triclinic

resolution	1.770 Å
resolution_low	44.220 Å
r_factor	0.1771
r_work	0.1749
r_free	0.2193

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