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9y4u

;Crystal structure of glyceraldehyde-3-phosphate dehydrogenase (GAPDH) from Neisseria gonorrhoeae in complex with NAD (Orthorhombic I form) ;

Method: X-RAY DIFFRACTION D_max: 97.2 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9y4u
deposition_date	2025-09-03
last_revision	2025-09-17
title	;Crystal structure of glyceraldehyde-3-phosphate dehydrogenase (GAPDH) from Neisseria gonorrhoeae in complex with NAD (Orthorhombic I form) ;
keywords	SSGCID, STRUCTURAL GENOMICS, SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE, GAPDH, 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	29.25 Å
rg_electron	28.92 Å
i0	76205900.00
molecular_weight	68202.0 kDa
excluded_volume	85193 Å³
envelope_volume	103270 Å³
shell_volume	31134 Å³
envelope_diameter	99.2 Å
shell_rg	34.79 Å
envelope_rg	28.90 Å
shape_rg	28.96 Å
total_rg	29.34 Å
total_atoms	4787
n_residues	629
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	97.2 Å
rg_real	29.38 Å
rg_real_error	0.85 Å
i0_real	7.6210e+07
i0_real_error	1.1580e+06
rg_reciprocal	29.33 Å
i0_reciprocal	76200000.0000
total_estimate	0.8684
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	27.0 Å
skewness	0.451
kurtosis	-0.429
angular_range	— – 0.2700 Å⁻¹
current_alpha	0.0000
highest_alpha	45340000.0000
n_real_points	55
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.826; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.920; Smooth: 0.886

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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	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	5087

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	2

Entity 3 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	267

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6. Citations (1)

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length_a	87.189 Å
length_b	123.985 Å
length_c	130.745 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	16

space_group	I 2 2 2
int_tables_number	23
crystal_system	—

resolution	1.900 Å
resolution_low	48.190 Å
r_factor	0.1769
r_work	0.1750
r_free	0.2144

fit	/app/data/saxs_computation/y4/9y4u/9y4u.fit
pddf	/app/data/pr_computation/y4/9y4u/9y4u.pr.out
profile	/app/data/saxs_computation/y4/9y4u/9y4u.dat

;Crystal structure of glyceraldehyde-3-phosphate dehydrogenase (GAPDH) from Neisseria gonorrhoeae in complex with NAD (Orthorhombic I form) ;

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