SAXSdb — 9wbe

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

Chalcone synthase

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 heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 1–395 Chain B； UniProt 1–395	Non-standard monomer：Yes (specific site not provided by mmCIF)	Probable chalcone--flavanone isomerase 3 × 2 （Q8VZW3）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；293 K；0.2 M trimethylamine N-oxide dihydrate, 0.1 M Tris pH 8.5, 20% (w/v) polyethylene glycol monomethyl ether 2000	Resolution 1.91 Å R-free 0.204

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 9WBE	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
6DXB Crystal structure of chalcone synthase from Arabidopsis thaliana Deposited 2018-06-28	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–395（395 aa） Chain C 1–395（395 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；0.1 M HEPES (pH 7.5), 0.3 M ammonium acetate, 14% (v/v) PEG 8000, and 5 mM DTT	Resolution 1.55 Å R-free 0.163
6DXB Crystal structure of chalcone synthase from Arabidopsis thaliana Deposited 2018-06-28	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain B 1–395（395 aa） Chain D 1–395（395 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；0.1 M HEPES (pH 7.5), 0.3 M ammonium acetate, 14% (v/v) PEG 8000, and 5 mM DTT	Resolution 1.55 Å R-free 0.163
6DXD Crystal structure of chalcone synthase from Arabidopsis thaliana - C347S mutant Deposited 2018-06-28	Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–395（395 aa） Chain C 1–395（395 aa）	Mutation：C347S Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：C347S Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；0.1 M HEPES (pH 7.5), 0.3 M ammonium acetate, 14% (v/v) PEG 8000, and 5 mM DTT	Resolution 1.59 Å R-free 0.169
6DXD Crystal structure of chalcone synthase from Arabidopsis thaliana - C347S mutant Deposited 2018-06-28	Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain B 1–395（395 aa） Chain D 1–395（395 aa）	Mutation：C347S Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：C347S Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；0.1 M HEPES (pH 7.5), 0.3 M ammonium acetate, 14% (v/v) PEG 8000, and 5 mM DTT	Resolution 1.59 Å R-free 0.169
6DXE Crystal structure of chalcone synthase from Arabidopsis thaliana - M64I F170S G173A S213G Q217A T270V C347S mutant Deposited 2018-06-28	Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–395（395 aa） Chain C 1–395（395 aa）	Mutation：M64I, F170S, G173A, S213G, Q217A, T270V, C347S Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：M64I, F170S, G173A, S213G, Q217A, T270V, C347S Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；0.125 NaSCN, 20% (v/v) PEG 3350, and 5 mM DTT	Resolution 1.61 Å R-free 0.202

3 other PDB entries and 5 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	CHSY_ARATH
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–395； UniProt 1–395 Author chain B； PDBConstruct 1–395； UniProt 1–395

Probable chalcone--flavanone isomerase 3

Arabidopsis thaliana

UniProt Q8VZW3

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 heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain C； UniProt 1–209 Chain D； UniProt 1–209	Not recorded	Chalcone synthase × 2 （P13114）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；293 K；0.2 M trimethylamine N-oxide dihydrate, 0.1 M Tris pH 8.5, 20% (w/v) polyethylene glycol monomethyl ether 2000	Resolution 1.91 Å R-free 0.204

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.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence

UniProt name	CFI3_ARATH
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain C； PDBConstruct 1–209； UniProt 1–209 Author chain D； PDBConstruct 1–209； UniProt 1–209

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	9wbe
Deposition date deposition_date	2025-08-13
Structure title title	Crystal structure of the CHS-CHIL complex
Keywords keywords	flavonoids biosynthesis, chalcone synthase, chalcone isomerase, CHS complex, 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	33.22 Å
Radius of gyration Rg (electron density) rg_electron	32.43 Å
Forward intensity I(0) i0	261014000.00
Molecular weight molecular_weight	131310.0 kDa
Excluded volume excluded_volume	165070 Å³
Envelope volume envelope_volume	201180 Å³
Hydration-shell volume shell_volume	50790 Å³
Envelope diameter envelope_diameter	124.2 Å
Shell Rg shell_rg	40.09 Å
Envelope Rg envelope_rg	32.68 Å
Shape Rg shape_rg	32.43 Å
Total Rg total_rg	32.97 Å
Total atoms total_atoms	15243
Residues n_residues	1190
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	116.8 Å
Rg (real space) rg_real	33.14 Å
Rg uncertainty (real space) rg_real_error	0.93 Å
I(0) (real space) i0_real	2.6100e+08
I(0) uncertainty (real space) i0_real_error	5.1380e+06
Rg (reciprocal space) rg_reciprocal	33.17 Å
I(0) (reciprocal space) i0_reciprocal	261000000.0000
Solution quality estimate total_estimate	0.8593
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	41.4 Å
Skewness Skewness skewness	0.330
Kurtosis Kurtosis kurtosis	-0.137
Angular range angular_range	— – 0.2400 Å⁻¹
Current regularization parameter α current_alpha	0.0002
Highest regularization parameter α highest_alpha	135400000.0000
Real-space data points n_real_points	49
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.729; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.991; Smooth: 0.989

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Chalcone synthase
Molecular weight formula_weight	43202.7 kDa
EC 编号 ec_number	2.3.1.74
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	16123

MVMAGASSLDEIRQAQRADGPAGILAIGTANPENHVLQAEYPDYYFRITNSEHMTDLKEKFKRMCDKSTIRKRHMHLTEEFLKENPHMCAYMAPSLDTRQDIVVVEVPKLGKEAAVKAIKEWGQPKSKITHVVFCTTSGVDMPGADYQLTKLLGLRPSVKRLMMYQQGCFAGGTVLRIAKDLAENNRGARVLVVCSEITAVTFRGPSDTHLDSLVGQALFSDGAAALIVGSDPDTSVGEKPIFEMVSAAQTILPDSDGAIDGHLREVGLTFHLLKDVPGLISKNIVKSLDEAFKPLGISDWNSLFWIAHPGGPAILDQVEIKLGLKEEKMRATRHVLSEYGNMSSACVLFILDEMRRKSAKDGVATTGEGLEWGVLFGFGPGLTVETVVLHSVPL

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 polymer

Description description	Probable chalcone--flavanone isomerase 3
Molecular weight formula_weight	23357.5 kDa
EC 编号 ec_number	5.5.1.6
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,D

MGTEMVMVHEVPFPPQIITSKPLSLLGQGITDIEIHFLQVKFTAIGVYLDPSDVKTHLDNWKGKTGKELAGDDDFFDALASAEMEKVIRVVVIKEIKGAQYGVQLENTVRDRLAEEDKYEEEEETELEKVVGFFQSKYFKANSVITYHFSAKDGICEIGFETEGKEEEKLKVENANVVGMMQRWYLSGSRGVSPSTIVSIADSISAVLT

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 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	808

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8. Citations (1)

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Unit-cell length a length_a	73.460 Å
Unit-cell length b length_b	114.910 Å
Unit-cell length c length_c	146.170 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 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	1.910 Å
Low-resolution limit resolution_low	34.990 Å
R factor r_factor	0.1713
R_work r_work	0.1696
R_free r_free	0.2044

fit	/app/data/saxs_computation/wb/9wbe/9wbe.fit
pddf	/app/data/pr_computation/wb/9wbe/9wbe.pr.out
profile	/app/data/saxs_computation/wb/9wbe/9wbe.dat

Crystal structure of the CHS-CHIL complex

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

Chalcone synthase

State in the Current Structure

Other States of the Same Protein in the Database

Probable chalcone--flavanone isomerase 3

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

6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 water

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)