← Back to search

9ywi

Crystal structure of a Glyceraldehyde-3-phosphate dehydrogenase from Bordetella pertussis (monoclinic P form)

Method: X-RAY DIFFRACTION D_max: 165.1 Å Quality: GOOD

SAXS Profile

P(r) Distribution

▼

1. Structure Basics

entry_id	9ywi
deposition_date	2025-10-24
last_revision	2025-11-05
title	Crystal structure of a Glyceraldehyde-3-phosphate dehydrogenase from Bordetella pertussis (monoclinic P form)
keywords	;SSGCID, STRUCTURAL GENOMICS, SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE, Glyceraldehyde-3-phosphate dehydrogenase, OXIDOREDUCTASE ;; OXIDOREDUCTASE
method	X-RAY DIFFRACTION

▼

Download Data

SAXS curve (.dat) P(r) distribution (.pr.out) Structure (CIF)

▼

2. SAXS Parameters (CRYSOL)

rg_guinier	49.98 Å
rg_electron	50.25 Å
i0	1235580000.00
molecular_weight	292970.0 kDa
excluded_volume	367090 Å³
envelope_volume	481170 Å³
shell_volume	79990 Å³
envelope_diameter	164.1 Å
shell_rg	52.86 Å
envelope_rg	49.59 Å
shape_rg	50.24 Å
total_rg	50.34 Å
total_atoms	20589
n_residues	2697
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

▼

3. P(r) Analysis (GNOM)

dmax	165.1 Å
rg_real	50.24 Å
rg_real_error	1.56 Å
i0_real	1.2360e+09
i0_real_error	2.1600e+07
rg_reciprocal	49.99 Å
i0_reciprocal	1235000000.0000
total_estimate	0.8059
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	51.6 Å
skewness	0.382
kurtosis	-0.625
angular_range	— – 0.1600 Å⁻¹
current_alpha	0.0000
highest_alpha	105400000.0000
n_real_points	33
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.835; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.969; Smooth: 0.000

▶

4. Crystallography & Experiment

▶

5. Entities & Polymer Info (8)

Entity 1 polymer

description	Glyceraldehyde-3-phosphate dehydrogenase
formula_weight	37360.5 kDa
ec_number	1.2.1.-
src_method	man
entity_count	8

Polymer

type	polypeptide(L)
strand_id	A,B,C,D,E,F,G,H
atom_count	22450

MAHHHHHHMTIRVVINGYGRIGRNILRAHYENGKKHDIEIVAINDLGDPKTNAHLTRFDTAHGKFPGTVTVDGDYMVVNGDKIRVLANRNPAELPWGELGVDVVLECTGFFTSKEKAGAHLKGGAKKVIISAPGGKDVDATIVFGVNQNVLKAEHTVISNASCTTNCLAPLVKPLHDKLGVETGLMTTVHAYTNDQVLTDVYHEDLRRARSATMSMIPTKTGAAAAVGLVLPELNGKLDGFAIRVPTINVSLVDLSFVAKRDTTVEEVNSILQAAAEGELKDILTYNTEPLVSIDFNHNPASSNFDATLTKVSGKLVKVSSWYDNEWGFSNRMLDTTVALMSAK

Source

organism	Bordetella pertussis Tohama I
ncbi_taxonomy_id	257313
host_organism	Escherichia coli BL21(DE3)

Entity 2 non-polymer

description	MAGNESIUM ION
formula_weight	24.3 kDa
src_method	syn
entity_count	12

Entity 3 non-polymer

description	TRIETHYLENE GLYCOL
formula_weight	150.2 kDa
src_method	syn
entity_count	9

Entity 4 non-polymer

description	TETRAETHYLENE GLYCOL
formula_weight	194.2 kDa
src_method	syn
entity_count	4

Entity 5 non-polymer

description	DI(HYDROXYETHYL)ETHER
formula_weight	106.1 kDa
src_method	syn
entity_count	10

Entity 6 non-polymer

description	GLYCEROL
formula_weight	92.1 kDa
src_method	syn
entity_count	1

Entity 7 non-polymer

description	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
formula_weight	122.1 kDa
src_method	syn
entity_count	1

Entity 8 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	1780

▶

6. Citations (1)

▶

length_a	81.467 Å
length_b	122.984 Å
length_c	150.567 Å
angle_alpha	90.00 °
angle_beta	90.11 °
angle_gamma	90.00 °
z_pdb	16

space_group	P 1 21 1
int_tables_number	4
crystal_system	—

resolution	2.000 Å
resolution_low	49.080 Å
r_factor	0.1710
r_work	0.1693
r_free	0.2033

fit	/app/data/saxs_computation/yw/9ywi/9ywi.fit
pddf	/app/data/pr_computation/yw/9ywi/9ywi.pr.out
profile	/app/data/saxs_computation/yw/9ywi/9ywi.dat