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9rb1

Streptococcus pyogenes GapN in complex with 2-cyanoacetamide

Method: X-RAY DIFFRACTION D_max: 171.0 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9rb1
deposition_date	2025-05-21
title	Streptococcus pyogenes GapN in complex with 2-cyanoacetamide
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	51.23 Å
rg_electron	51.01 Å
i0	2243820000.00
molecular_weight	405940.0 kDa
excluded_volume	512460 Å³
envelope_volume	660040 Å³
shell_volume	105310 Å³
envelope_diameter	185.7 Å
shell_rg	56.32 Å
envelope_rg	50.30 Å
shape_rg	51.00 Å
total_rg	51.21 Å
total_atoms	57566
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	171.0 Å
rg_real	51.24 Å
rg_real_error	1.43 Å
i0_real	2.2440e+09
i0_real_error	4.1170e+07
rg_reciprocal	51.22 Å
i0_reciprocal	2244000000.0000
total_estimate	0.8713
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	60.7 Å
skewness	0.392
kurtosis	-0.230
angular_range	— – 0.1550 Å⁻¹
current_alpha	0.0000
highest_alpha	263000000.0000
n_real_points	32
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.835; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.817

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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	62835

ASWSHPQFEKIEGRRDRGPEFLAKQYKNLVNGEWKLSENEITIYAPATGEELGSVPAMTQAEVDAVYASAKKALSDWRTLSYVERAAYLHKAADILVRDAEKIGAILSKEVAKGHKAAVSEVIRTAEIINYAAEEGLRMEGEVLEGGSFEAASKKKIAIVRREPVGLVLAISPFNYPVNLAGSKIAPALIAGNVVALKPPTQGSISGLLLAEAFAEAGIPAGVFNTITGRGSVIGDYIVEHEAVNFINFTGSTPIGEGIGKLAGMRPIMLELGGKDSAIVLEDADLALAAKNIVAGAFGYSGQRSTAVKRVLVMDKVADQLAAEIKTLVEKLSVGMPEDDADITPLIDTSAADFVEGLIKDATDKGATALTAFNREGNLISPVLFDHVTTDMRLAWEEPFGPVLPIIRVTTVEEAIKISNESEYGLQASIFTTNFPKAFGIAEQLEVGTVHLNNKTQRGTDNFPFLGAKKSGAGVQGVKYSIEAMTTVKSVVFDIQ

Source

organism	Streptococcus pyogenes
ncbi_taxonomy_id	1314
host_organism	Escherichia coli

Entity 2 non-polymer

description	2-cyanoacetamide
formula_weight	84.1 kDa
src_method	syn
entity_count	12

Entity 3 non-polymer

description	SULFATE ION
formula_weight	96.1 kDa
src_method	syn
entity_count	16

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	4475

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6. Citations (1)

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length_a	98.517 Å
length_b	99.583 Å
length_c	104.162 Å
angle_alpha	77.66 °
angle_beta	75.94 °
angle_gamma	67.67 °
z_pdb	8

space_group	P 1
int_tables_number	1
crystal_system	triclinic

resolution	1.610 Å
resolution_low	47.920 Å
r_factor	0.1589
r_work	0.1571
r_free	0.1932

fit	/app/data/saxs_computation/rb/9rb1/9rb1.fit
pddf	/app/data/pr_computation/rb/9rb1/9rb1.pr.out
profile	/app/data/saxs_computation/rb/9rb1/9rb1.dat