;Crystal strcture of adenosylcobinamide kinase/adenosylcobinamide phosphate guanylyltransferase CobU H49A from Akkermansia muciniphila in complex with GTP ;

entry_id	9vit
deposition_date	2025-06-18
last_revision	2025-10-08
title	;Crystal strcture of adenosylcobinamide kinase/adenosylcobinamide phosphate guanylyltransferase CobU H49A from Akkermansia muciniphila in complex with GTP ;
keywords	;VB12, Cobamide remodeling, CobU, adenosylcobinamide kinase, adenosylcobinamide phosphate guanylyltransferase, Akkermansia muciniphila, TRANSFERASE ;; TRANSFERASE
method	X-RAY DIFFRACTION

rg_guinier	24.93 Å
rg_electron	24.08 Å
i0	58396300.00
molecular_weight	58636.0 kDa
excluded_volume	73199 ų
envelope_volume	86906 ų
shell_volume	29640 ų
envelope_diameter	79.5 Å
shell_rg	31.78 Å
envelope_rg	24.37 Å
shape_rg	24.12 Å
total_rg	24.81 Å
total_atoms	4104
n_residues	527
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	86.1 Å
rg_real	24.80 Å
rg_real_error	0.60 Å
i0_real	5.8400e+07
i0_real_error	8.5020e+05
rg_reciprocal	24.83 Å
i0_reciprocal	58400000.0000
total_estimate	0.7953
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	28.7 Å
skewness	0.196
kurtosis	-0.514
angular_range	— – 0.3200 Å−1
current_alpha	0.0000
highest_alpha	15450000.0000
n_real_points	64
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.786; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.977; Smooth: 0.000

Unit Cell

length_a	52.740 Å
length_b	55.533 Å
length_c	97.807 Å
angle_alpha	90.00 °
angle_beta	100.95 °
angle_gamma	90.00 °
z_pdb	6

Symmetry

space_group	P 1 21 1
int_tables_number	4
crystal_system	—

Refinement

resolution	2.400 Å
resolution_low	49.690 Å
r_factor	0.2309
r_work	0.2288
r_free	0.2688

Diffraction

temperature

100.0 K

Files (7)

• pr_distribution /app/data/pr_computation/vi/9vit/pr_distribution.json
• pr_output /app/data/pr_computation/vi/9vit/9vit.pr.out
• pr_plot /app/data/visualization/pr_computation/vi/9vit/9vit_pr_distribution.png
• saxs_curve_dat /app/data/saxs_computation/vi/9vit/9vit.dat
• saxs_fit /app/data/saxs_computation/vi/9vit/9vit.fit
• saxs_log /app/data/saxs_computation/vi/9vit/9vit.log
• saxs_plot /app/data/visualization/saxs_computation/vi/9vit/9vit_saxs_profile.png

Curves (3)

fit	/app/data/saxs_computation/vi/9vit/9vit.fit
pddf	/app/data/pr_computation/vi/9vit/9vit.pr.out
profile	/app/data/saxs_computation/vi/9vit/9vit.dat