Crystal structure of PpNeuA CMP-Kdn synthetase

Method: X-RAY DIFFRACTION D_max: 81.6 Å Quality: GOOD

SAXS Profile

P(r) Distribution

▼

1. Structure Basics

entry_id	9t4z
deposition_date	2025-11-03
title	Crystal structure of PpNeuA CMP-Kdn synthetase
keywords	CMP-Kdn synthetase, LIGASE; LIGASE
method	X-RAY DIFFRACTION

▼

Download Data

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

▼

2. SAXS Parameters (CRYSOL)

rg_guinier	25.33 Å
rg_electron	24.44 Å
i0	42206400.00
molecular_weight	50064.0 kDa
excluded_volume	62658 Å³
envelope_volume	75818 Å³
shell_volume	26539 Å³
envelope_diameter	84.3 Å
shell_rg	31.18 Å
envelope_rg	24.22 Å
shape_rg	24.42 Å
total_rg	25.28 Å
total_atoms	7012
n_residues	445
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	81.6 Å
rg_real	25.36 Å
rg_real_error	0.44 Å
i0_real	4.2210e+07
i0_real_error	5.2550e+05
rg_reciprocal	25.35 Å
i0_reciprocal	42210000.0000
total_estimate	0.8900
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	27.2 Å
skewness	0.387
kurtosis	-0.430
angular_range	— – 0.3150 Å⁻¹
current_alpha	0.0001
highest_alpha	12180000.0000
n_real_points	64
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.874; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.966; Smooth: 0.979

▶

4. Crystallography & Experiment

▶

5. Entities & Polymer Info (2)

▶

6. Citations (2)

▶

length_a	56.432 Å
length_b	47.782 Å
length_c	87.850 Å
angle_alpha	90.00 °
angle_beta	102.12 °
angle_gamma	90.00 °
z_pdb	4

space_group	P 1 21 1
int_tables_number	4
crystal_system	monoclinic

resolution	1.800 Å
resolution_low	51.610 Å
r_factor	0.1882
r_work	0.1867
r_free	0.2154

description	PpNeuA
formula_weight	28261.3 kDa
src_method	man
entity_count	2

type	polypeptide(L)
strand_id	A,B
atom_count	7256

Crystal structure of PpNeuA CMP-Kdn synthetase

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 (2)

Entity 1 polymer

Polymer

Source

Entity 2 water

6. Citations (2)

7. Files & Curves (10)

Files (7)

Curves (3)

organism	Prymnesium parvum
ncbi_taxonomy_id	97485
host_organism	Escherichia coli

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	244

fit	/app/data/saxs_computation/t4/9t4z/9t4z.fit
pddf	/app/data/pr_computation/t4/9t4z/9t4z.pr.out
profile	/app/data/saxs_computation/t4/9t4z/9t4z.dat