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9zao

Crystal structure of a glyceraldehyde-3-phosphate dehydrogenase from Neisseria gonorrhoeae in complex with NAD (P1 form2)

Method: X-RAY DIFFRACTION D_max: 215.6 Å Quality: REASONABLE

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9zao
deposition_date	2025-11-19
last_revision	2025-12-24
title	Crystal structure of a glyceraldehyde-3-phosphate dehydrogenase from Neisseria gonorrhoeae in complex with NAD (P1 form2)
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	73.17 Å
rg_electron	73.43 Å
i0	7208340000.00
molecular_weight	709860.0 kDa
excluded_volume	884680 Å³
envelope_volume	1286000 Å³
shell_volume	146550 Å³
envelope_diameter	244.8 Å
shell_rg	72.18 Å
envelope_rg	71.28 Å
shape_rg	73.44 Å
total_rg	73.39 Å
total_atoms	49857
n_residues	6646
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	215.6 Å
rg_real	73.16 Å
rg_real_error	1.20 Å
i0_real	7.2020e+09
i0_real_error	1.3750e+08
rg_reciprocal	72.55 Å
i0_reciprocal	7197000000.0000
total_estimate	0.6178
solution_quality	REASONABLE a REASONABLE solution
n_peaks	1
r_peak_primary	92.4 Å
skewness	0.353
kurtosis	-0.438
angular_range	— – 0.1050 Å⁻¹
current_alpha	0.0041
highest_alpha	262100000.0000
n_real_points	22
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.985; Stabil: 0.999; Sysdev: 0.020; Positv: 1.000; Valcen: 0.998; Smooth: 0.017

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4. Crystallography & Experiment

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5. Entities & Polymer Info (3)

Entity 1 polymer

description	Glyceraldehyde-3-phosphate dehydrogenase
formula_weight	36829.8 kDa
ec_number	1.2.1.-
src_method	man
entity_count	20

Polymer

type	polypeptide(L)
strand_id	A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,S,T
atom_count	49857

MAHHHHHHMSIKVAINGFGRIGRLALRQIEKAHGIEVAAVNDLTPAEMLLHLFKYDSTQGRFQGTAELKDDAIVVNGREIKVFANPNPEELPWGELGVDVVLECTGFFTNKTKAEAHIRAGARKVVISAPGGNDVKTVVYGVNQDILDGSETVISAASCTTNCLAPMAAVLQKEFGVVEGLMTTIHAYTGDQNTLDAPHRKGDLRRARAAALNIVPNSTGAAKAIGLVIPELNGKLDGSAQRVPVATGSLTELVSVLERPATKEEINAAMKAASSESYGYNEDQIVSSDVVGIEYGSLFDATQTRVMTVGGKQLVKTVAWYDNEMSYTCQLVRTLEYFAGKI

Source

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

Entity 2 non-polymer

description	NICOTINAMIDE-ADENINE-DINUCLEOTIDE
formula_weight	663.4 kDa
src_method	syn
entity_count	13

Entity 3 non-polymer

description	SODIUM ION
formula_weight	23.0 kDa
src_method	syn
entity_count	4

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6. Citations (1)

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length_a	76.358 Å
length_b	139.715 Å
length_c	222.702 Å
angle_alpha	76.30 °
angle_beta	87.32 °
angle_gamma	88.12 °
z_pdb	20

space_group	P 1
int_tables_number	1
crystal_system	—

resolution	3.090 Å
resolution_low	48.290 Å
r_factor	0.1834
r_work	0.1809
r_free	0.2335

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

Crystal structure of a glyceraldehyde-3-phosphate dehydrogenase from Neisseria gonorrhoeae in complex with NAD (P1 form2)

SAXS Profile

P(r) Distribution

1. Structure Basics

Download Data

2. SAXS Parameters (CRYSOL)

3. P(r) Analysis (GNOM)

4. Crystallography & Experiment

Unit Cell

Symmetry

Refinement

Diffraction