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9uya

Crystal structure of phospholipase D form Streptomyces avermitilis

Method: X-RAY DIFFRACTION D_max: 125.0 Å Quality: REASONABLE

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9uya
deposition_date	2025-05-15
last_revision	2026-05-13
title	Crystal structure of phospholipase D form Streptomyces avermitilis
keywords	Phospholipase D, Alkaline phosphatase, 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	41.55 Å
rg_electron	41.08 Å
i0	773734000.00
molecular_weight	223780.0 kDa
excluded_volume	277450 Å³
envelope_volume	342750 Å³
shell_volume	68245 Å³
envelope_diameter	128.2 Å
shell_rg	47.57 Å
envelope_rg	40.50 Å
shape_rg	41.09 Å
total_rg	41.33 Å
total_atoms	15783
n_residues	2041
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	125.0 Å
rg_real	41.32 Å
rg_real_error	0.72 Å
i0_real	7.7370e+08
i0_real_error	1.1950e+07
rg_reciprocal	41.55 Å
i0_reciprocal	773900000.0000
total_estimate	0.6752
solution_quality	REASONABLE a REASONABLE solution
n_peaks	1
r_peak_primary	59.2 Å
skewness	0.010
kurtosis	-0.662
angular_range	— – 0.1900 Å⁻¹
current_alpha	0.0000
highest_alpha	180300000.0000
n_real_points	39
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.951; Stabil: 1.000; Sysdev: 0.046; Positv: 1.000; Valcen: 0.987; Smooth: 0.796

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

Entity 1 polymer

description	Alkaline phosphatase, secereted
formula_weight	57276.6 kDa
src_method	man
entity_count	4

Polymer

type	polypeptide(L)
strand_id	A,B,C,D
atom_count	16553

MATETPAFLHGVASGDPLPDGILLWTRVTPTAEAIPGSGLGPDTEVSWTVAKDKTFTAIVAKGSTTATAASDHTVKADIRGLQPATDYFFRFSAGGTDSPVARTRTAPAADAGVAGLRFGVVSCANWEAGYFSPYRHLAARGDLDAWLHLGDYIYEYKSGEYAARGKVVRPHAPANEILTLADYRTRHGRYKTDPDLQALHHKAPVVAIWDDHEFADNAWSGGAGNHTEGAEGTWTARQAAAKQAYFEWMPVRPAIEGTTYRRLRFGKLADLSLLDLRSFRSQQASTGSGTVDDPERTLTGRVQLDWLKAGLKASDTTWRLVGNSVMISPFAIGELSADLFKPLAKLLGLPQEGIALNTDQWDGYTDDRRELLAHLRNNAIRNTVFLTGDIHMAWANDVPFDAGTYPLSASAGTEFVVTSVTSDNLDDIVKVPEGTVSAVAAPLIRAANRHVHWVDTDRHGYGVLDITADRAQMDYYVLSDRTDPNATSSWARSYRTRSGTQKVERTYDPVKLAAALEHHHHHH

Source

organism	Streptomyces avermitilis MA-4680 = NBRC 14893
ncbi_taxonomy_id	227882
host_organism	Escherichia coli BL21(DE3)

Entity 2 non-polymer

description	FE (III) ION
formula_weight	55.8 kDa
src_method	syn
entity_count	4

Entity 3 non-polymer

description	CALCIUM ION
formula_weight	40.1 kDa
src_method	syn
entity_count	20

Entity 4 non-polymer

description	PHOSPHATE ION
formula_weight	95.0 kDa
src_method	syn
entity_count	4

Entity 5 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	770

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6. Citations (1)

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length_a	90.938 Å
length_b	156.810 Å
length_c	163.756 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	16

space_group	P 21 21 21
int_tables_number	19
crystal_system	orthorhombic

resolution	2.200 Å
resolution_low	46.800 Å
r_factor	0.1792
r_work	0.1775
r_free	0.2111

fit	/app/data/saxs_computation/uy/9uya/9uya.fit
pddf	/app/data/pr_computation/uy/9uya/9uya.pr.out
profile	/app/data/saxs_computation/uy/9uya/9uya.dat