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9xwv

Crystal structure of E.coli CDP-diacylglycerol pyrophosphatase (Cdh) complexed with CMP

Method: X-RAY DIFFRACTION D_max: 83.3 Å Quality: REASONABLE

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9xwv
deposition_date	2025-11-28
title	Crystal structure of E.coli CDP-diacylglycerol pyrophosphatase (Cdh) complexed with CMP
keywords	;CDP-diacylglycerol, Phosphatidic acid, Bitopic membrane protein, CDP-DAG hydrolase, bacterial phospholipid metabolism, CMP bound structure, byproduct bound, 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	25.36 Å
rg_electron	24.61 Å
i0	46912400.00
molecular_weight	51110.0 kDa
excluded_volume	63239 Å³
envelope_volume	75900 Å³
shell_volume	25905 Å³
envelope_diameter	83.6 Å
shell_rg	31.69 Å
envelope_rg	24.64 Å
shape_rg	24.62 Å
total_rg	25.38 Å
total_atoms	3588
n_residues	442
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	83.3 Å
rg_real	25.37 Å
rg_real_error	0.56 Å
i0_real	4.6910e+07
i0_real_error	6.5350e+05
rg_reciprocal	25.37 Å
i0_reciprocal	46910000.0000
total_estimate	0.7096
solution_quality	REASONABLE a REASONABLE solution
n_peaks	1
r_peak_primary	26.5 Å
skewness	0.363
kurtosis	-0.433
angular_range	— – 0.3150 Å⁻¹
current_alpha	0.0000
highest_alpha	6882000.0000
n_real_points	64
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.851; Stabil: 1.000; Sysdev: 0.242; Positv: 1.000; Valcen: 0.961; Smooth: 0.981

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4. Crystallography & Experiment

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5. Entities & Polymer Info (3)

Entity 1 polymer

description	CDP-diacylglycerol pyrophosphatase
formula_weight	29427.7 kDa
ec_number	3.6.1.26
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	3765

MKKAGLLFLVMIVIAVVAAGIGYWKLTGEESDTLRKIVLEECLPNQQQNQNPSPCAEVKPNAGYVVLKDLNGPLQYLLMPTYRINGTESPLLTDPSTPNFFWLAWQARDFMSKKYGQPVPDRAVSLAINSRTGRTQNHFHIHISCIRPDVRKQLDNNLANISSRWLPLPGGLRGHEYLARRVTESELVQRSPFMMLAEEVPEAREHMGRYGLAMVRQSDNSFVLLATQRNLLTLNRASAEEIQDHQCEILRGHHHHHHG

Source

organism	Escherichia coli K-12
ncbi_taxonomy_id	83333
host_organism	Escherichia coli BL21(DE3)

Entity 2 non-polymer

description	CYTIDINE-5'-MONOPHOSPHATE
formula_weight	323.2 kDa
src_method	syn
entity_count	2

Entity 3 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	154

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6. Citations (1)

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length_a	68.958 Å
length_b	54.088 Å
length_c	81.989 Å
angle_alpha	90.00 °
angle_beta	93.14 °
angle_gamma	90.00 °
z_pdb	4

space_group	P 1 21 1
int_tables_number	4
crystal_system	—

resolution	1.940 Å
resolution_low	42.530 Å
r_factor	0.1881
r_work	0.1857
r_free	0.2350

fit	/app/data/saxs_computation/xw/9xwv/9xwv.fit
pddf	/app/data/pr_computation/xw/9xwv/9xwv.pr.out
profile	/app/data/saxs_computation/xw/9xwv/9xwv.dat

Crystal structure of E.coli CDP-diacylglycerol pyrophosphatase (Cdh) complexed with CMP

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