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9xdg

Glyoxysomal Citrate Synthase 3 from Arabidopsis thaliana in complex with OAA and MNB

Method: X-RAY DIFFRACTION D_max: 87.6 Å Quality: EXCELLENT

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9xdg
deposition_date	2025-10-27
title	Glyoxysomal Citrate Synthase 3 from Arabidopsis thaliana in complex with OAA and MNB
keywords	citrate synthase, glyoxysome, glyoxylate cycle, Arabidopsis, TRANSFERASE; 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	28.53 Å
rg_electron	27.67 Å
i0	135646000.00
molecular_weight	94321.0 kDa
excluded_volume	118970 Å³
envelope_volume	141440 Å³
shell_volume	40938 Å³
envelope_diameter	90.9 Å
shell_rg	36.69 Å
envelope_rg	27.91 Å
shape_rg	27.66 Å
total_rg	28.53 Å
total_atoms	6647
n_residues	842
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	87.6 Å
rg_real	28.41 Å
rg_real_error	0.43 Å
i0_real	1.3560e+08
i0_real_error	1.9710e+06
rg_reciprocal	28.47 Å
i0_reciprocal	135700000.0000
total_estimate	0.9036
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	2
r_peak_primary	34.4 Å
skewness	0.203
kurtosis	-0.483
angular_range	— – 0.2800 Å⁻¹
current_alpha	0.0000
highest_alpha	37650000.0000
n_real_points	57
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.936; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.992; Smooth: 0.943

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4. Crystallography & Experiment

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5. Entities & Polymer Info (8)

Entity 1 polymer

description	Citrate synthase 3, peroxisomal
formula_weight	52786.2 kDa
ec_number	2.3.3.16
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	6862

GPLGSDTSVAPLGSLKGTLTIVDERTGKNYKVPVSDDGTVKAVDFKKIVTGKEDKGLKLYDPGYLNTAPVRSSISYIDGDEGILRYRGYPIEEMAENSTFLEVAYLLMYGNLPSESQLSDWEFAVSQHSAVPQGVLDIIQSMPHDAHPMGVLVSAMSALSIFHPDANPALRGQDIYDSKQVRDKQIIRIIGKAPTIAAAAYLRMAGRPPVLPSGNLPYADNFLYMLDSLGNRSYKPNPRLARVLDILFILHAEHEMNCSTAAARHLASSGVDVYTAVAGAVGALYGPLHGGANEAVLKMLSEIGTVENIPEFIEGVKNRKRKMSGFGHRVYKNYDPRAKVIKNLADEVFSIVGKDPLIEVAVALEKAALSDDYFVKRKLYPNVDFYSGLIYRAMGFPPEFFTVLFAIPRMAGYLSHWKESLDDPDTKIMRPQQVYTGVWLRHYTPVRERIVTDDSKESDKLGQVATSNASRRRLAGSSV

Source

organism	Arabidopsis thaliana
common_name	thale cress
ncbi_taxonomy_id	3702
host_organism	Escherichia coli

Entity 2 non-polymer

description	MAGNESIUM ION
formula_weight	24.3 kDa
src_method	syn
entity_count	2

Entity 3 non-polymer

description	5-MERCAPTO-2-NITRO-BENZOIC ACID
formula_weight	199.2 kDa
src_method	syn
entity_count	2

Entity 4 non-polymer

description	DI(HYDROXYETHYL)ETHER
formula_weight	106.1 kDa
src_method	syn
entity_count	1

Entity 5 non-polymer

description	1,2-ETHANEDIOL
formula_weight	62.1 kDa
src_method	syn
entity_count	4

Entity 6 non-polymer

description	OXALOACETATE ION
formula_weight	131.1 kDa
src_method	syn
entity_count	1

Entity 7 non-polymer

description	TETRAETHYLENE GLYCOL
formula_weight	194.2 kDa
src_method	syn
entity_count	1

Entity 8 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	207

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6. Citations (1)

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length_a	192.336 Å
length_b	63.550 Å
length_c	76.595 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	2.294 Å
resolution_low	38.915 Å
r_factor	—
r_work	0.2042
r_free	0.2658

fit	/app/data/saxs_computation/xd/9xdg/9xdg.fit
pddf	/app/data/pr_computation/xd/9xdg/9xdg.pr.out
profile	/app/data/saxs_computation/xd/9xdg/9xdg.dat