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9raz

Streptococcus pyogenes GapN in complex with NADP and glyceraldehyde-3-phosphate

Method: X-RAY DIFFRACTION D_max: 169.4 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9raz
deposition_date	2025-05-21
title	Streptococcus pyogenes GapN in complex with NADP and glyceraldehyde-3-phosphate
keywords	GapN, NADP, G3H, Substrate, OXIDOREDUCTASE; 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	50.56 Å
rg_electron	50.39 Å
i0	2241700000.00
molecular_weight	406510.0 kDa
excluded_volume	513460 Å³
envelope_volume	648360 Å³
shell_volume	104450 Å³
envelope_diameter	184.3 Å
shell_rg	56.03 Å
envelope_rg	49.75 Å
shape_rg	50.38 Å
total_rg	50.59 Å
total_atoms	57669
n_residues	3800
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	169.4 Å
rg_real	50.56 Å
rg_real_error	1.76 Å
i0_real	2.2420e+09
i0_real_error	4.6870e+07
rg_reciprocal	50.56 Å
i0_reciprocal	2242000000.0000
total_estimate	0.8711
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	60.1 Å
skewness	0.387
kurtosis	-0.213
angular_range	— – 0.1550 Å⁻¹
current_alpha	0.0000
highest_alpha	233600000.0000
n_real_points	32
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.827; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.838

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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	64525

ASWSHPQFEKIEGRRDRGPEFLAKQYKNLVNGEWKLSENEITIYAPATGEELGSVPAMTQAEVDAVYASAKKALSDWRTLSYVERAAYLHKAADILVRDAEKIGAILSKEVAKGHKAAVSEVIRTAEIINYAAEEGLRMEGEVLEGGSFEAASKKKIAIVRREPVGLVLAISPFNYPVNLAGSKIAPALIAGNVVALKPPTQGSISGLLLAEAFAEAGIPAGVFNTITGRGSVIGDYIVEHEAVNFINFTGSTPIGEGIGKLAGMRPIMLELGGKDSAIVLEDADLALAAKNIVAGAFGYSGQRSTAVKRVLVMDKVADQLAAEIKTLVEKLSVGMPEDDADITPLIDTSAADFVEGLIKDATDKGATALTAFNREGNLISPVLFDHVTTDMRLAWEEPFGPVLPIIRVTTVEEAIKISNESEYGLQASIFTTNFPKAFGIAEQLEVGTVHLNNKTQRGTDNFPFLGAKKSGAGVQGVKYSIEAMTTVKSVVFDIQ

Source

organism	Streptococcus pyogenes
ncbi_taxonomy_id	1314
host_organism	Escherichia coli BL21

Entity 2 non-polymer

description	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
formula_weight	743.4 kDa
src_method	syn
entity_count	4

Entity 3 non-polymer

description	GLYCEROL
formula_weight	92.1 kDa
src_method	syn
entity_count	3

Entity 4 non-polymer

description	GLYCERALDEHYDE-3-PHOSPHATE
formula_weight	170.1 kDa
src_method	syn
entity_count	1

Entity 5 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	3980

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6. Citations (1)

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length_a	97.150 Å
length_b	97.435 Å
length_c	100.710 Å
angle_alpha	77.06 °
angle_beta	78.19 °
angle_gamma	68.92 °
z_pdb	8

space_group	P 1
int_tables_number	1
crystal_system	triclinic

resolution	1.380 Å
resolution_low	48.620 Å
r_factor	0.1553
r_work	0.1541
r_free	0.1792

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