;Crystal structure of thiamine pyrophosphate (TPP)-dependent alpha-imino acid decarboxylase (AzcB and AzcC) from Streptomyces mobaraensis in complex with TTPP and 6-amino-4-oxo-4,5-dihydro-1,3,5-triazine-2-carboxylic acid. ;

entry_id	9u8r
deposition_date	2025-03-26
last_revision	2026-04-01
title	;Crystal structure of thiamine pyrophosphate (TPP)-dependent alpha-imino acid decarboxylase (AzcB and AzcC) from Streptomyces mobaraensis in complex with TTPP and 6-amino-4-oxo-4,5-dihydro-1,3,5-triazine-2-carboxylic acid. ;
keywords	;thiamine pyrophosphate (TPP)-dependent decarboxylase, AzcB, AzcC, 5-azacytidine biosynthesis, 6-amino-4-oxo-4, 5-dihydro-1, 3, 5-triazine-2-carboxylic acid, LYASE ;; LYASE
method	X-RAY DIFFRACTION

rg_guinier	37.12 Å
rg_electron	36.76 Å
i0	1729950000.00
molecular_weight	220390.0 kDa
excluded_volume	209070 ų
envelope_volume	342760 ų
shell_volume	72477 ų
envelope_diameter	123.5 Å
shell_rg	46.41 Å
envelope_rg	36.77 Å
shape_rg	36.84 Å
total_rg	36.99 Å
total_atoms	16518
n_residues	2166
n_harmonics	20
q_range	— – 0.5000 Å−1
n_points	101
shell_type	directional
solvent_density	0.3340 e/ų
contrast_shell	0.0300 e/ų
crysol_version	4.1.3

dmax	114.0 Å
rg_real	36.90 Å
rg_real_error	0.81 Å
i0_real	1.7300e+09
i0_real_error	2.9050e+07
rg_reciprocal	37.04 Å
i0_reciprocal	1730000000.0000
total_estimate	0.9006
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	2
r_peak_primary	47.7 Å
skewness	0.166
kurtosis	-0.497
angular_range	— – 0.2150 Å−1
current_alpha	0.0000
highest_alpha	439600000.0000
n_real_points	44
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.928; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.984; Smooth: 0.938

Unit Cell

length_a	274.162 Å
length_b	158.845 Å
length_c	73.869 Å
angle_alpha	90.00 °
angle_beta	99.20 °
angle_gamma	90.00 °
z_pdb	24

Symmetry

space_group	C 1 2 1
int_tables_number	5
crystal_system	monoclinic

Refinement

resolution	2.550 Å
resolution_low	48.020 Å
r_factor	0.1920
r_work	0.1912
r_free	0.2278

Diffraction

temperature

100.0 K

Files (7)

• pr_distribution /app/data/pr_computation/u8/9u8r/pr_distribution.json
• pr_output /app/data/pr_computation/u8/9u8r/9u8r.pr.out
• pr_plot /app/data/visualization/pr_computation/u8/9u8r/9u8r_pr_distribution.png
• saxs_curve_dat /app/data/saxs_computation/u8/9u8r/9u8r.dat
• saxs_fit /app/data/saxs_computation/u8/9u8r/9u8r.fit
• saxs_log /app/data/saxs_computation/u8/9u8r/9u8r.log
• saxs_plot /app/data/visualization/saxs_computation/u8/9u8r/9u8r_saxs_profile.png

Curves (3)

fit	/app/data/saxs_computation/u8/9u8r/9u8r.fit
pddf	/app/data/pr_computation/u8/9u8r/9u8r.pr.out
profile	/app/data/saxs_computation/u8/9u8r/9u8r.dat