Crystal structure of YgdH from Neisseria meningitidis

Method: X-RAY DIFFRACTION D_max: 83.0 Å Quality: EXCELLENT

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9us2
deposition_date	2025-05-01
title	Crystal structure of YgdH from Neisseria meningitidis
keywords	;Cytokinin riboside 5'-monophosphate phosphoribohydrolase with a strong preference for UMP, HYDROLASE ;; HYDROLASE
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	27.46 Å
rg_electron	26.35 Å
i0	69880900.00
molecular_weight	66084.0 kDa
excluded_volume	83026 Å³
envelope_volume	101330 Å³
shell_volume	31948 Å³
envelope_diameter	86.4 Å
shell_rg	33.74 Å
envelope_rg	26.23 Å
shape_rg	26.34 Å
total_rg	27.17 Å
total_atoms	4671
n_residues	612
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	83.0 Å
rg_real	27.35 Å
rg_real_error	0.38 Å
i0_real	6.9880e+07
i0_real_error	7.8880e+05
rg_reciprocal	27.38 Å
i0_reciprocal	69880000.0000
total_estimate	0.9125
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	2
r_peak_primary	35.8 Å
skewness	0.181
kurtosis	-0.562
angular_range	— – 0.2900 Å⁻¹
current_alpha	0.0000
highest_alpha	18400000.0000
n_real_points	59
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.971; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.946

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4. Crystallography & Experiment

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5. Entities & Polymer Info (3)

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6. Citations (1)

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length_a	86.814 Å
length_b	142.236 Å
length_c	119.308 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	24

space_group	C 2 2 21
int_tables_number	20
crystal_system	—

resolution	1.800 Å
resolution_low	24.980 Å
r_factor	0.2080
r_work	0.2069
r_free	0.2285

description	;Cytokinin riboside 5'-monophosphate phosphoribohydrolase ;
formula_weight	22712.7 kDa
ec_number	3.2.2.-
src_method	man
entity_count	3

type	polypeptide(L)
strand_id	A,B,C
atom_count	4895

Crystal structure of YgdH from Neisseria meningitidis

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

5. Entities & Polymer Info (3)

Entity 1 polymer

Polymer

Source

Entity 2 non-polymer

Entity 3 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)

organism	Neisseria meningitidis
ncbi_taxonomy_id	487
host_organism	Escherichia coli BL21(DE3)

description	CITRIC ACID
formula_weight	192.1 kDa
src_method	syn
entity_count	1

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	224

fit	/app/data/saxs_computation/us/9us2/9us2.fit
pddf	/app/data/pr_computation/us/9us2/9us2.pr.out
profile	/app/data/saxs_computation/us/9us2/9us2.dat