← Back to search

9z9c

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

Method: X-RAY DIFFRACTION D_max: 219.7 Å Quality: GOOD

SAXS Profile

P(r) Distribution

▼

1. Structure Basics

entry_id	9z9c
deposition_date	2025-11-18
last_revision	2025-11-26
title	Crystal structure of a glyceraldehyde-3-phosphate dehydrogenase from Neisseria gonorrhoeae in complex with NAD (P1 form)
keywords	SSGCID, STRUCTURAL GENOMICS, SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE, OXIDOREDUCTASE; OXIDOREDUCTASE
method	X-RAY DIFFRACTION

▼

Download Data

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

▼

2. SAXS Parameters (CRYSOL)

rg_guinier	67.59 Å
rg_electron	67.47 Å
i0	10460500000.00
molecular_weight	852600.0 kDa
excluded_volume	1061500 Å³
envelope_volume	1504500 Å³
shell_volume	179630 Å³
envelope_diameter	235.0 Å
shell_rg	73.64 Å
envelope_rg	65.33 Å
shape_rg	67.47 Å
total_rg	67.53 Å
total_atoms	59850
n_residues	7897
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	219.7 Å
rg_real	67.40 Å
rg_real_error	2.12 Å
i0_real	1.0460e+10
i0_real_error	2.1630e+08
rg_reciprocal	68.14 Å
i0_reciprocal	10470000000.0000
total_estimate	0.8564
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	95.5 Å
skewness	0.157
kurtosis	-0.314
angular_range	— – 0.1150 Å⁻¹
current_alpha	0.0000
highest_alpha	1230000000.0000
n_real_points	24
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.834; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.974; Smooth: 0.656

▶

4. Crystallography & Experiment

▶

5. Entities & Polymer Info (4)

Entity 1 polymer

description	Glyceraldehyde-3-phosphate dehydrogenase
formula_weight	36829.8 kDa
ec_number	1.2.1.-
src_method	man
entity_count	24

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,U,V,W,X
atom_count	60606

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	24

Entity 3 non-polymer

description	TRIETHYLENE GLYCOL
formula_weight	150.2 kDa
src_method	syn
entity_count	1

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	756

▶

6. Citations (1)

▶

length_a	105.534 Å
length_b	137.842 Å
length_c	157.786 Å
angle_alpha	85.95 °
angle_beta	77.63 °
angle_gamma	86.88 °
z_pdb	24

space_group	P 1
int_tables_number	1
crystal_system	—

resolution	2.300 Å
resolution_low	48.530 Å
r_factor	0.1958
r_work	0.1939
r_free	0.2316

fit	/app/data/saxs_computation/z9/9z9c/9z9c.fit
pddf	/app/data/pr_computation/z9/9z9c/9z9c.pr.out
profile	/app/data/saxs_computation/z9/9z9c/9z9c.dat

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