SAXSdb — 9x0i

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Citrate synthase 3, peroxisomal

Arabidopsis thaliana

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 36–509 Chain B； UniProt 36–509	Not recorded	OAA OXALOACETATE ION × 2 COA COENZYME A × 2 PEG DI(HYDROXYETHYL)ETHER × 2 MG MAGNESIUM ION × 5 EDO 1,2-ETHANEDIOL × 1 EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；20mM CoA and 20mM OAA in 90mM HEPES pH7.0, 9mM MgCl2, 18%(w/v) PEG3350	Resolution 1.70 Å R-free 0.197

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 9X0I	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
9XAU Glyoxysomal Citrate Synthase 3 from Arabidopsis thaliana in complex with OAA Deposited 2025-10-23	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 36–509（474 aa） Chain B 36–509（474 aa）	Not recorded	OAA OXALOACETATE ION × 2 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；100mM OAA, 65mM HEPES pH 7.0, 6.5mM MgCl2, 13% (w/v) PEG3350	Resolution 1.95 Å R-free 0.225
9XAU Glyoxysomal Citrate Synthase 3 from Arabidopsis thaliana in complex with OAA Deposited 2025-10-23	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 36–509（474 aa） Chain D 36–509（474 aa）	Not recorded	OAA OXALOACETATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；100mM OAA, 65mM HEPES pH 7.0, 6.5mM MgCl2, 13% (w/v) PEG3350	Resolution 1.95 Å R-free 0.225
9XDG Glyoxysomal Citrate Synthase 3 from Arabidopsis thaliana in complex with OAA and MNB Deposited 2025-10-27	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 36–509（474 aa） Chain B 36–509（474 aa）	Not recorded	MG MAGNESIUM ION × 2 MNB 5-MERCAPTO-2-NITRO-BENZOIC ACID × 2 PEG DI(HYDROXYETHYL)ETHER × 1 EDO 1,2-ETHANEDIOL × 4 OAA OXALOACETATE ION × 1 PG4 TETRAETHYLENE GLYCOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；100mM OAA and 10% volume of a saturated solution of DNTB in 70mM HEPES pH7.0, 7mM MgCl2, 14%(w/v) PEG3350	Resolution 2.29 Å R-free 0.266

2 other PDB entries and 3 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	CISY3_ARATH
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 6–479； UniProt 36–509 Author chain B； PDBConstruct 6–479； UniProt 36–509

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	9x0i
Deposition date deposition_date	2025-09-30
Structure title title	Glyoxysomal Citrate Synthase 3 from Arabidopsis thaliana in complex with OAA and CoA
Keywords keywords	citrate synthase, glyoxysome, glyoxylate cycle, Arabidopsis, TRANSFERASE; TRANSFERASE
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	28.73 Å
Radius of gyration Rg (electron density) rg_electron	27.85 Å
Forward intensity I(0) i0	156063000.00
Molecular weight molecular_weight	100150.0 kDa
Excluded volume excluded_volume	125850 Å³
Envelope volume envelope_volume	148680 Å³
Hydration-shell volume shell_volume	42453 Å³
Envelope diameter envelope_diameter	95.1 Å
Shell Rg shell_rg	37.01 Å
Envelope Rg envelope_rg	28.13 Å
Shape Rg shape_rg	27.85 Å
Total Rg total_rg	28.70 Å
Total atoms total_atoms	7044
Residues n_residues	881
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	89.5 Å
Rg (real space) rg_real	28.60 Å
Rg uncertainty (real space) rg_real_error	0.52 Å
I(0) (real space) i0_real	1.5610e+08
I(0) uncertainty (real space) i0_real_error	2.1790e+06
Rg (reciprocal space) rg_reciprocal	28.66 Å
I(0) (reciprocal space) i0_reciprocal	156100000.0000
Solution quality estimate total_estimate	0.9017
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	87.9 Å
Skewness Skewness skewness	0.191
Kurtosis Kurtosis kurtosis	-0.463
Angular range angular_range	— – 0.2750 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	40250000.0000
Real-space data points n_real_points	56
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.913; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.993; Smooth: 0.986

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (8)

Entity 1 Entity 1 polymer

Description description	Citrate synthase 3, peroxisomal
Molecular weight formula_weight	52786.2 kDa
EC 编号 ec_number	2.3.3.16
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	7902

GPLGSDTSVAPLGSLKGTLTIVDERTGKNYKVPVSDDGTVKAVDFKKIVTGKEDKGLKLYDPGYLNTAPVRSSISYIDGDEGILRYRGYPIEEMAENSTFLEVAYLLMYGNLPSESQLSDWEFAVSQHSAVPQGVLDIIQSMPHDAHPMGVLVSAMSALSIFHPDANPALRGQDIYDSKQVRDKQIIRIIGKAPTIAAAAYLRMAGRPPVLPSGNLPYADNFLYMLDSLGNRSYKPNPRLARVLDILFILHAEHEMNCSTAAARHLASSGVDVYTAVAGAVGALYGPLHGGANEAVLKMLSEIGTVENIPEFIEGVKNRKRKMSGFGHRVYKNYDPRAKVIKNLADEVFSIVGKDPLIEVAVALEKAALSDDYFVKRKLYPNVDFYSGLIYRAMGFPPEFFTVLFAIPRMAGYLSHWKESLDDPDTKIMRPQQVYTGVWLRHYTPVRERIVTDDSKESDKLGQVATSNASRRRLAGSSV

来源 Source

来源生物 organism	Arabidopsis thaliana
通用名 common_name	thale cress
NCBI Class编号 ncbi_taxonomy_id	3702
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	OXALOACETATE ION
Molecular weight formula_weight	131.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	COENZYME A
Molecular weight formula_weight	767.5 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	DI(HYDROXYETHYL)ETHER
Molecular weight formula_weight	106.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	5

Entity 6 Entity 6 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 7 Entity 7 non-polymer

Description description	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
Molecular weight formula_weight	238.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 8 Entity 8 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	787

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8. Citations (1)

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Unit-cell length a length_a	193.859 Å
Unit-cell length b length_b	60.597 Å
Unit-cell length c length_c	76.864 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 21 21 2
Space-group number int_tables_number	18
Crystal system crystal_system	—

Resolution resolution	1.700 Å
Low-resolution limit resolution_low	38.320 Å
R factor r_factor	—
R_work r_work	0.1659
R_free r_free	0.1967

fit	/app/data/saxs_computation/x0/9x0i/9x0i.fit
pddf	/app/data/pr_computation/x0/9x0i/9x0i.pr.out
profile	/app/data/saxs_computation/x0/9x0i/9x0i.dat

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

1. Protein Identity and Related Structures Protein Identity & Related Structures

Citrate synthase 3, peroxisomal

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction