6dxd

Crystal structure of chalcone synthase from Arabidopsis thaliana - C347S mutant

Method: X-RAY DIFFRACTION D_max: 130.2 Å Quality: GOOD

▼

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 homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 1–395 Chain C； UniProt 1–395	Mutation：C347S Non-standard monomer：Yes (specific site not provided by mmCIF)	No other associated polymer	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
2	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain B； UniProt 1–395 Chain D； UniProt 1–395	Mutation：C347S Non-standard monomer：Yes (specific site not provided by mmCIF)	No other associated polymer	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

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 6DXD	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 mutation/modification 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 mutation/modification 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
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 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
9WBE Crystal structure of the CHS-CHIL complex Deposited 2025-08-13	Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–395（395 aa） Chain B 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, 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

3 other PDB entries and 4 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 Author chain C； PDBConstruct 1–395； UniProt 1–395 Author chain D； PDBConstruct 1–395； UniProt 1–395

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.

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	6dxd
Deposition date deposition_date	2018-06-28
Structure title title	Crystal structure of chalcone synthase from Arabidopsis thaliana - C347S mutant
Keywords keywords	Thiolase, Flavonoid, Polyketide synthase, TRANSFERASE; TRANSFERASE
Experimental Method method	X-RAY DIFFRACTION

▼

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

Radius of gyration Rg (Guinier) rg_guinier	39.40 Å
Radius of gyration Rg (electron density) rg_electron	39.07 Å
Forward intensity I(0) i0	427851000.00
Molecular weight molecular_weight	170260.0 kDa
Excluded volume excluded_volume	213780 Å³
Envelope volume envelope_volume	262930 Å³
Hydration-shell volume shell_volume	55942 Å³
Envelope diameter envelope_diameter	136.6 Å
Shell Rg shell_rg	44.78 Å
Envelope Rg envelope_rg	38.82 Å
Shape Rg shape_rg	39.08 Å
Total Rg total_rg	39.34 Å
Total atoms total_atoms	24008
Residues n_residues	1552
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

▼

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

Maximum dimension Dmax dmax	130.2 Å
Rg (real space) rg_real	39.52 Å
Rg uncertainty (real space) rg_real_error	0.91 Å
I(0) (real space) i0_real	4.2790e+08
I(0) uncertainty (real space) i0_real_error	7.8820e+06
Rg (reciprocal space) rg_reciprocal	39.45 Å
I(0) (reciprocal space) i0_reciprocal	427800000.0000
Solution quality estimate total_estimate	0.8782
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	39.0 Å
Skewness Skewness skewness	0.372
Kurtosis Kurtosis kurtosis	-0.507
Angular range angular_range	— – 0.2000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	119700000.0000
Real-space data points n_real_points	41
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.876; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.961; Smooth: 0.823

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Description description	Chalcone synthase
Molecular weight formula_weight	43186.6 kDa
EC 编号 ec_number	2.3.1.74
Mutation mutation	C347S
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	25972

MVMAGASSLDEIRQAQRADGPAGILAIGTANPENHVLQAEYPDYYFRITNSEHMTDLKEKFKRMCDKSTIRKRHMHLTEEFLKENPHMCAYMAPSLDTRQDIVVVEVPKLGKEAAVKAIKEWGQPKSKITHVVFCTTSGVDMPGADYQLTKLLGLRPSVKRLMMYQQGCFAGGTVLRIAKDLAENNRGARVLVVCSEITAVTFRGPSDTHLDSLVGQALFSDGAAALIVGSDPDTSVGEKPIFEMVSAAQTILPDSDGAIDGHLREVGLTFHLLKDVPGLISKNIVKSLDEAFKPLGISDWNSLFWIAHPGGPAILDQVEIKLGLKEEKMRATRHVLSEYGNMSSASVLFILDEMRRKSAKDGVATTGEGLEWGVLFGFGPGLTVETVVLHSVPL

来源 Source

来源生物 organism	Arabidopsis thaliana
通用名 common_name	Mouse-ear cress
NCBI Class编号 ncbi_taxonomy_id	3702
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	1825

▼

7. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

Domain ID domain_id	d6dxda1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.95 — Thiolase-like
Superfamily Superfamily superfamily	c.95.1 — Thiolase-like
Family Family family	c.95.1.2 — Chalcone synthase-like

Domain ID domain_id	d6dxda2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.95 — Thiolase-like
Superfamily Superfamily superfamily	c.95.1 — Thiolase-like
Family Family family	c.95.1.2 — Chalcone synthase-like

Domain ID domain_id	d6dxdb1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.95 — Thiolase-like
Superfamily Superfamily superfamily	c.95.1 — Thiolase-like
Family Family family	c.95.1.2 — Chalcone synthase-like

Domain ID domain_id	d6dxdb2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.95 — Thiolase-like
Superfamily Superfamily superfamily	c.95.1 — Thiolase-like
Family Family family	c.95.1.2 — Chalcone synthase-like

Domain ID domain_id	d6dxdc1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.95 — Thiolase-like
Superfamily Superfamily superfamily	c.95.1 — Thiolase-like
Family Family family	c.95.1.2 — Chalcone synthase-like

Domain ID domain_id	d6dxdc2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.95 — Thiolase-like
Superfamily Superfamily superfamily	c.95.1 — Thiolase-like
Family Family family	c.95.1.2 — Chalcone synthase-like

Domain ID domain_id	d6dxdd1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.95 — Thiolase-like
Superfamily Superfamily superfamily	c.95.1 — Thiolase-like
Family Family family	c.95.1.2 — Chalcone synthase-like

Domain ID domain_id	d6dxdd2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.95 — Thiolase-like
Superfamily Superfamily superfamily	c.95.1 — Thiolase-like
Family Family family	c.95.1.2 — Chalcone synthase-like

CATH v4.4 (8 domains)

Domain ID domain_id	6dxdA01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	47 — Peroxisomal Thiolase; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — Thiolase/Chalcone synthase

Domain ID domain_id	6dxdA02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	47 — Peroxisomal Thiolase; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — Thiolase/Chalcone synthase

Domain ID domain_id	6dxdB01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	47 — Peroxisomal Thiolase; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — Thiolase/Chalcone synthase

Domain ID domain_id	6dxdB02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	47 — Peroxisomal Thiolase; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — Thiolase/Chalcone synthase

Domain ID domain_id	6dxdC01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	47 — Peroxisomal Thiolase; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — Thiolase/Chalcone synthase

Domain ID domain_id	6dxdC02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	47 — Peroxisomal Thiolase; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — Thiolase/Chalcone synthase

Domain ID domain_id	6dxdD01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	47 — Peroxisomal Thiolase; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — Thiolase/Chalcone synthase

Domain ID domain_id	6dxdD02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	47 — Peroxisomal Thiolase; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — Thiolase/Chalcone synthase

▶

8. Citations (1)

▶

Unit-cell length a length_a	54.860 Å
Unit-cell length b length_b	138.220 Å
Unit-cell length c length_c	108.900 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	95.73 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	1.590 Å
Low-resolution limit resolution_low	32.920 Å
R factor r_factor	0.1453
R_work r_work	0.1451
R_free r_free	0.1685

fit	/app/data/saxs_computation/dx/6dxd/6dxd.fit
pddf	/app/data/pr_computation/dx/6dxd/6dxd.pr.out
profile	/app/data/saxs_computation/dx/6dxd/6dxd.dat