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9u39

Crystal structure of Serine Acetyltransferase (SAT) from Planctomyces limnophilus in complex with its substrate serine

Method: X-RAY DIFFRACTION D_max: 81.0 Å Quality: EXCELLENT

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9u39
deposition_date	2025-03-18
last_revision	2026-03-18
title	Crystal structure of Serine Acetyltransferase (SAT) from Planctomyces limnophilus in complex with its substrate serine
keywords	Transferase, hexapeptide repeat; TRANSFERASE
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	28.40 Å
rg_electron	27.06 Å
i0	158599000.00
molecular_weight	98873.0 kDa
excluded_volume	123490 Å³
envelope_volume	146960 Å³
shell_volume	42547 Å³
envelope_diameter	86.0 Å
shell_rg	36.53 Å
envelope_rg	27.25 Å
shape_rg	27.05 Å
total_rg	27.96 Å
total_atoms	6979
n_residues	888
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	81.0 Å
rg_real	28.13 Å
rg_real_error	0.30 Å
i0_real	1.5860e+08
i0_real_error	2.0400e+06
rg_reciprocal	28.21 Å
i0_reciprocal	158600000.0000
total_estimate	0.9120
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	2
r_peak_primary	37.6 Å
skewness	0.041
kurtosis	-0.577
angular_range	— – 0.2800 Å⁻¹
current_alpha	0.0000
highest_alpha	49110000.0000
n_real_points	57
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.974; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.972; Smooth: 0.957

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

Entity 1 polymer

description	Serine O-acetyltransferase
formula_weight	34688.3 kDa
ec_number	2.3.1.30
src_method	man
entity_count	3

Polymer

type	polypeptide(L)
strand_id	A,B,C
atom_count	7117

MATDLRLKDQLPEITDRIVESYRDFATTHHLGHCPLPSSEAVYEIAQDLQEILFPGYRRRQNLHMGNVTYHVGDLVDSLHDRLTQQIARALRHDYRRQHGISCADEVSHDFEALAQAKTITLLELLPRLRRTLALDVQAAFDGDPAAGSLDEIIFCYPGLHAVTIYRLAHELYLLDVPLIPRMLTEWAHSQTGIDIHPGATIGHSFFIDHGTGVVIGETCEIANHVKLYQGVTLGALSFPKDEQGNLLRRHKRHPTIEDHVVIYANATVLGGETVIGSHAVIGSSVSLSHSVPPNTIVTIEKPSLRYREAS

Source

organism	Planctopirus limnophila DSM 3776
ncbi_taxonomy_id	521674
host_organism	Escherichia coli BL21(DE3)

Entity 2 non-polymer

description	GLYCEROL
formula_weight	92.1 kDa
src_method	syn
entity_count	7

Entity 3 non-polymer

description	SODIUM ION
formula_weight	23.0 kDa
src_method	syn
entity_count	1

Entity 4 non-polymer

description	SERINE
formula_weight	105.1 kDa
src_method	syn
entity_count	3

Entity 5 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	138

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6. Citations (1)

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length_a	104.980 Å
length_b	90.030 Å
length_c	122.544 Å
angle_alpha	90.00 °
angle_beta	114.80 °
angle_gamma	90.00 °
z_pdb	12

space_group	I 1 2 1
int_tables_number	5
crystal_system	—

resolution	2.218 Å
resolution_low	40.858 Å
r_factor	—
r_work	0.2131
r_free	0.2692

fit	/app/data/saxs_computation/u3/9u39/9u39.fit
pddf	/app/data/pr_computation/u3/9u39/9u39.pr.out
profile	/app/data/saxs_computation/u3/9u39/9u39.dat