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9yd8

Crystal structure of Phospholipase D (PLD) from Arcanobacterium haemolyticum

Method: X-RAY DIFFRACTION D_max: 74.5 Å Quality: EXCELLENT

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9yd8
deposition_date	2025-09-22
title	Crystal structure of Phospholipase D (PLD) from Arcanobacterium haemolyticum
keywords	sphingomyelinase D, hydrolase, Arcanobacterium haemolyticum, thermostability, phospholipase D, TOXIN; 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	24.65 Å
rg_electron	23.40 Å
i0	66925200.00
molecular_weight	62242.0 kDa
excluded_volume	77133 Å³
envelope_volume	89357 Å³
shell_volume	30969 Å³
envelope_diameter	76.5 Å
shell_rg	31.24 Å
envelope_rg	23.35 Å
shape_rg	23.35 Å
total_rg	24.35 Å
total_atoms	4395
n_residues	547
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	74.5 Å
rg_real	24.51 Å
rg_real_error	0.43 Å
i0_real	6.6930e+07
i0_real_error	9.4060e+05
rg_reciprocal	24.54 Å
i0_reciprocal	66930000.0000
total_estimate	0.9060
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	2
r_peak_primary	30.8 Å
skewness	0.198
kurtosis	-0.439
angular_range	— – 0.3200 Å⁻¹
current_alpha	0.0000
highest_alpha	12350000.0000
n_real_points	64
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.934; Stabil: 0.997; Sysdev: 1.000; Positv: 1.000; Valcen: 0.990; Smooth: 0.989

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	Phospholipase D
formula_weight	33710.4 kDa
ec_number	3.1.4.-,3.1.4.41
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	4414

MGSSHHHHHHENLYFQGQEQPTTGNRPVYAIAHRVLTKQSVDDAIKIGANALEIDFTAWRRGWWADHDGLPTSAGDTAEDILKYIAQKRREGNNITFVWFDIKNPDYCKDQNSVCSITKLRDLARQTIEQEGVRALFGFYKTVGGVGWNTIANNLNDKEAVALSGRKDDIMKDFKQYENKIKPQQRVADNGYYNLSYGFGGCYRDENQTCDQLRLAGEERKKGNLGKTFGWTVSTGQEYLAADLLNKAEVDGMIFGFKTTYFYDHADTRNAFAGIKNWVDAHQGTHHMATNKDIPW

Source

organism	Arcanobacterium haemolyticum
ncbi_taxonomy_id	28264
host_organism	Escherichia coli

Entity 2 non-polymer

description	GLYCEROL
formula_weight	92.1 kDa
src_method	syn
entity_count	2

Entity 3 non-polymer

description	MAGNESIUM ION
formula_weight	24.3 kDa
src_method	syn
entity_count	2

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	19

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6. Citations (1)

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length_a	94.289 Å
length_b	96.704 Å
length_c	61.731 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	8

space_group	P 21 21 2
int_tables_number	18
crystal_system	—

resolution	2.450 Å
resolution_low	67.510 Å
r_factor	0.2326
r_work	0.2291
r_free	0.2990

fit	/app/data/saxs_computation/yd/9yd8/9yd8.fit
pddf	/app/data/pr_computation/yd/9yd8/9yd8.pr.out
profile	/app/data/saxs_computation/yd/9yd8/9yd8.dat

Crystal structure of Phospholipase D (PLD) from Arcanobacterium haemolyticum

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