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9zag

;Crystal structure of a glyceraldehyde-3-phosphate dehydrogenase from Neisseria gonorrhoeae in complex with NAD and GLYCERALDEHYDE-3-PHOSPHATE ;

Method: X-RAY DIFFRACTION D_max: 158.6 Å Quality: REASONABLE

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9zag
deposition_date	2025-11-19
last_revision	2025-12-03
title	;Crystal structure of a glyceraldehyde-3-phosphate dehydrogenase from Neisseria gonorrhoeae in complex with NAD and GLYCERALDEHYDE-3-PHOSPHATE ;
keywords	;SSGCID, STRUCTURAL GENOMICS, SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE, glyceraldehyde-3-phosphate dehydrogenase, 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	46.08 Å
rg_electron	46.25 Å
i0	1294260000.00
molecular_weight	293400.0 kDa
excluded_volume	365270 Å³
envelope_volume	456480 Å³
shell_volume	81212 Å³
envelope_diameter	158.5 Å
shell_rg	51.26 Å
envelope_rg	45.81 Å
shape_rg	46.26 Å
total_rg	46.38 Å
total_atoms	20560
n_residues	2667
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	158.6 Å
rg_real	46.21 Å
rg_real_error	1.53 Å
i0_real	1.2940e+09
i0_real_error	2.3300e+07
rg_reciprocal	46.08 Å
i0_reciprocal	1294000000.0000
total_estimate	0.6580
solution_quality	REASONABLE a REASONABLE solution
n_peaks	1
r_peak_primary	46.6 Å
skewness	0.421
kurtosis	-0.384
angular_range	— – 0.1700 Å⁻¹
current_alpha	0.0000
highest_alpha	145700000.0000
n_real_points	35
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.791; Stabil: 1.000; Sysdev: 0.115; Positv: 1.000; Valcen: 0.999; Smooth: 0.833

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4. Crystallography & Experiment

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5. Entities & Polymer Info (10)

Entity 1 polymer

description	Glyceraldehyde-3-phosphate dehydrogenase
formula_weight	36829.8 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	21909

MAHHHHHHMSIKVAINGFGRIGRLALRQIEKAHGIEVAAVNDLTPAEMLLHLFKYDSTQGRFQGTAELKDDAIVVNGREIKVFANPNPEELPWGELGVDVVLECTGFFTNKTKAEAHIRAGARKVVISAPGGNDVKTVVYGVNQDILDGSETVISAASCTTNCLAPMAAVLQKEFGVVEGLMTTIHAYTGDQNTLDAPHRKGDLRRARAAALNIVPNSTGAAKAIGLVIPELNGKLDGSAQRVPVATGSLTELVSVLERPATKEEINAAMKAASSESYGYNEDQIVSSDVVGIEYGSLFDATQTRVMTVGGKQLVKTVAWYDNEMSYTCQLVRTLEYFAGKI

Source

organism	Neisseria gonorrhoeae NCCP11945
ncbi_taxonomy_id	521006
host_organism	Escherichia coli BL21(DE3)

Entity 2 non-polymer

description	GLYCERALDEHYDE-3-PHOSPHATE
formula_weight	170.1 kDa
src_method	syn
entity_count	8

Entity 3 non-polymer

description	DI(HYDROXYETHYL)ETHER
formula_weight	106.1 kDa
src_method	syn
entity_count	8

Entity 4 non-polymer

description	NICOTINAMIDE-ADENINE-DINUCLEOTIDE
formula_weight	663.4 kDa
src_method	syn
entity_count	8

Entity 5 non-polymer

description	SODIUM ION
formula_weight	23.0 kDa
src_method	syn
entity_count	8

Entity 6 non-polymer

description	TRIETHYLENE GLYCOL
formula_weight	150.2 kDa
src_method	syn
entity_count	1

Entity 7 non-polymer

description	CHLORIDE ION
formula_weight	35.5 kDa
src_method	syn
entity_count	1

Entity 8 non-polymer

description	GLYCEROL
formula_weight	92.1 kDa
src_method	syn
entity_count	2

Entity 9 non-polymer

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

Entity 10 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	1298

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6. Citations (1)

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length_a	68.647 Å
length_b	105.543 Å
length_c	167.699 Å
angle_alpha	90.00 °
angle_beta	94.63 °
angle_gamma	90.00 °
z_pdb	16

space_group	P 1 21 1
int_tables_number	4
crystal_system	—

resolution	1.910 Å
resolution_low	48.890 Å
r_factor	0.1563
r_work	0.1547
r_free	0.1870

fit	/app/data/saxs_computation/za/9zag/9zag.fit
pddf	/app/data/pr_computation/za/9zag/9zag.pr.out
profile	/app/data/saxs_computation/za/9zag/9zag.dat