PDB-9kah: Crystal Structure of Chalcone Syntase and Chalcone Isomerase-like...

ID or keywords:

Entry

Database: PDB / ID: 9kah

Title

Crystal Structure of Chalcone Syntase and Chalcone Isomerase-like Protein Complex from Physcomitrella patens

Components

Chalcone synthase
Chalcone-flavonone isomerase family protein

Keywords

TRANSFERASE / Flavonoid / Protein-Protein Complex / chalcone synthase / chalcone isomerase-like protein

Function / homology

Function and homology information

intramolecular lyase activity / chalcone synthase / naringenin-chalcone synthase activity / polyketide biosynthetic process / acyltransferase activity, transferring groups other than amino-acyl groups
Similarity search - Function

Biological species

Physcomitrium patens (plant)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.92 Å

Authors

Imaizumi, R. / Waki, T. / Yasuda, A. / Yanai, T. / Takeshita, K. / Sakai, N. / Yamamoto, M. / Nakayama, T. / Yamashita, S.

Funding support

Japan, 4items

Organization	Grant number	Country
Japan Society for the Promotion of Science (JSPS)	23H05470	Japan
Japan Society for the Promotion of Science (JSPS)	21H02115	Japan
Japan Society for the Promotion of Science (JSPS)	24K23286	Japan
Japan Agency for Medical Research and Development (AMED)	JP20am0101070	Japan

Citation

Journal: To Be Published
Title: Structural basis, dynamics, and mode of action of enhancer of flavonoid production in metabolon
Authors: Imaizumi, R. / Waki, T. / Yasuda, A. / Yanai, T. / Takeshita, K. / Sakai, N. / Yamamoto, M. / Nakayama, T. / Yamashita, S.

History

Deposition	Oct 28, 2024	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Oct 29, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	9kah.cif.gz	527.2 KB	Display	PDBx/mmCIF format
PDB format	pdb9kah.ent.gz	420.4 KB	Display	PDB format
PDBx/mmJSON format	9kah.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	9kah_validation.pdf.gz	520.1 KB	Display	wwPDB validaton report
Full document	9kah_full_validation.pdf.gz	529.2 KB	Display
Data in XML	9kah_validation.xml.gz	128.4 KB	Display
Data in CIF	9kah_validation.cif.gz	178.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ka/9kah ftp://data.pdbj.org/pub/pdb/validation_reports/ka/9kah	HTTPS FTP

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Related structure data

Related structure data	9kaiC 9kajC C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#90 - Jun 2007 Fatty Acid Synthase similarity (1) #216 - Dec 2017 Biodegradable Plastic similarity (1)

Deposited unit

A: Chalcone synthase

B: Chalcone synthase

C: Chalcone-flavonone isomerase family protein

D: Chalcone-flavonone isomerase family protein

E: Chalcone synthase

F: Chalcone synthase

G: Chalcone-flavonone isomerase family protein

H: Chalcone-flavonone isomerase family protein

hetero molecules

280 kDa, 8 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Chalcone synthase

B: Chalcone synthase

C: Chalcone-flavonone isomerase family protein

D: Chalcone-flavonone isomerase family protein

hetero molecules

defined by author&software
Evidence: gel filtration
140 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

E: Chalcone synthase

F: Chalcone synthase

G: Chalcone-flavonone isomerase family protein

H: Chalcone-flavonone isomerase family protein

hetero molecules

defined by author&software
140 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	79.900, 88.870, 117.970
Angle α, β, γ (deg.)	74.438, 74.318, 68.803
Int Tables number	1
Space group name H-M	P1

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	1	ALA	ALA	ASN	ASN	A	A	10 - 395	26 - 411
2	1	1	ALA	ALA	ASN	ASN	B	B	10 - 395	26 - 411
3	2	2	ALA	ALA	SER	SER	A	A	10 - 396	26 - 412
4	2	2	ALA	ALA	SER	SER	E	E	10 - 396	26 - 412
5	3	3	ARG	ARG	ASN	ASN	A	A	9 - 395	25 - 411
6	3	3	ARG	ARG	ASN	ASN	F	F	9 - 395	25 - 411
7	4	4	ALA	ALA	ASN	ASN	B	B	10 - 395	26 - 411
8	4	4	ALA	ALA	ASN	ASN	E	E	10 - 395	26 - 411
9	5	5	ALA	ALA	ASN	ASN	B	B	10 - 395	26 - 411
10	5	5	ALA	ALA	ASN	ASN	F	F	10 - 395	26 - 411
11	6	6	GLN	GLN	ALA	ALA	C	C	4 - 208	20 - 224
12	6	6	GLN	GLN	ALA	ALA	D	D	4 - 208	20 - 224
13	7	7	GLN	GLN	ALA	ALA	C	C	4 - 208	20 - 224
14	7	7	GLN	GLN	ALA	ALA	G	G	4 - 208	20 - 224
15	8	8	GLN	GLN	ALA	ALA	C	C	4 - 208	20 - 224
16	8	8	GLN	GLN	ALA	ALA	H	H	4 - 208	20 - 224
17	9	9	GLN	GLN	ALA	ALA	D	D	4 - 208	20 - 224
18	9	9	GLN	GLN	ALA	ALA	G	G	4 - 208	20 - 224
19	10	10	GLN	GLN	ALA	ALA	D	D	4 - 208	20 - 224
20	10	10	GLN	GLN	ALA	ALA	H	H	4 - 208	20 - 224
21	11	11	ALA	ALA	ASN	ASN	E	E	10 - 395	26 - 411
22	11	11	ALA	ALA	ASN	ASN	F	F	10 - 395	26 - 411
23	12	12	GLN	GLN	ALA	ALA	G	G	4 - 209	20 - 225
24	12	12	GLN	GLN	ALA	ALA	H	H	4 - 209	20 - 225

NCS ensembles :

ID	Details
1	Local NCS retraints between domains: 1 2
2	Local NCS retraints between domains: 3 4
3	Local NCS retraints between domains: 5 6
4	Local NCS retraints between domains: 7 8
5	Local NCS retraints between domains: 9 10
6	Local NCS retraints between domains: 11 12
7	Local NCS retraints between domains: 13 14
8	Local NCS retraints between domains: 15 16
9	Local NCS retraints between domains: 17 18
10	Local NCS retraints between domains: 19 20
11	Local NCS retraints between domains: 21 22
12	Local NCS retraints between domains: 23 24

#1: Protein	Chalcone synthase Mass: 44682.320 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Physcomitrium patens (plant) / Gene: PHYPA_029015 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q2VAZ3, chalcone synthase
#2: Protein	Chalcone-flavonone isomerase family protein Mass: 25317.420 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Physcomitrium patens (plant) / Gene: PHYPA_006757 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: A9SRW1
#3: Chemical	ChemComp-PEG / DI(HYDROXYETHYL)ETHER Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₄H₁₀O₃
#4: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: C₂H₆O₂
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 2644 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y
Has protein modification	Y

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.64 Å³/Da / Density % sol: 53.35 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: PEG 3350, potassium citrate

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 1 Å
Detector	Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Oct 19, 2023
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 1.92→50 Å / Num. obs: 216275 / % possible obs: 98.9 % / Redundancy: 2.89 % / CC_1/2: 0.986 / R_rim(I) all: 0.17 / Net I/σ(I): 5.16
Reflection shell	Resolution: 1.92→2.04 Å / Redundancy: 2.94 % / Mean I/σ(I) obs: 1.01 / Num. unique obs: 34942 / CC_1/2: 0.61 / R_rim(I) all: 1.13 / % possible all: 99.1

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Processing

Software

Name	Version	Classification
PHENIX	1.21.2-5419	refinement
REFMAC	5.8.0430	refinement
XDS		data reduction
XDS		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.92→49.186 Å / Cor.coef. F_o:F_c: 0.965 / Cor.coef. F_o:F_c free: 0.951 / Cross valid method: FREE R-VALUE / ESU R: 0.145 / ESU R Free: 0.133
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2126	10913	5.046 %
R_work	0.1773	205362	-
all	0.179	-	-
obs	-	216275	99.003 %

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 28.82 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.798 Å²	-0.806 Å²	-0.882 Å²
2-	-	-0.904 Å²	1.529 Å²
3-	-	-	1.166 Å²

Refinement step

Cycle: LAST / Resolution: 1.92→49.186 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	18156	0	26	2644	20826

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.01	0.012	18751
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.016	17999
X-RAY DIFFRACTION	r_angle_refined_deg	1.538	1.824	25428
X-RAY DIFFRACTION	r_angle_other_deg	0.709	1.748	41681
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.936	5	2415
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	3.723	5	83
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.28	10	3203
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	16.848	10	773
X-RAY DIFFRACTION	r_chiral_restr	0.178	0.2	2872
X-RAY DIFFRACTION	r_gen_planes_refined	0.004	0.02	21868
X-RAY DIFFRACTION	r_gen_planes_other	0.004	0.02	3928
X-RAY DIFFRACTION	r_nbd_refined	0.208	0.2	3773
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.213	0.2	16814
X-RAY DIFFRACTION	r_nbtor_refined	0.178	0.2	9409
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.08	0.2	9556
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.077	0.2	1495
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.095	0.2	11
X-RAY DIFFRACTION	r_nbd_other	0.182	0.2	48
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.076	0.2	27
X-RAY DIFFRACTION	r_mcbond_it	3.634	3.087	9618
X-RAY DIFFRACTION	r_mcbond_other	3.634	3.087	9618
X-RAY DIFFRACTION	r_mcangle_it	4.227	5.506	12047
X-RAY DIFFRACTION	r_mcangle_other	4.226	5.507	12048
X-RAY DIFFRACTION	r_scbond_it	4.945	3.397	9133
X-RAY DIFFRACTION	r_scbond_other	4.945	3.397	9134
X-RAY DIFFRACTION	r_scangle_it	6.269	6.059	13381
X-RAY DIFFRACTION	r_scangle_other	6.269	6.059	13382
X-RAY DIFFRACTION	r_lrange_it	6.702	30.533	21243
X-RAY DIFFRACTION	r_lrange_other	6.62	29.152	20557
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.088	0.05	12258
X-RAY DIFFRACTION	r_ncsr_local_group_2	0.088	0.05	12310
X-RAY DIFFRACTION	r_ncsr_local_group_3	0.091	0.05	12302
X-RAY DIFFRACTION	r_ncsr_local_group_4	0.088	0.05	12335
X-RAY DIFFRACTION	r_ncsr_local_group_5	0.092	0.05	12313
X-RAY DIFFRACTION	r_ncsr_local_group_6	0.117	0.05	6317
X-RAY DIFFRACTION	r_ncsr_local_group_7	0.123	0.05	6302
X-RAY DIFFRACTION	r_ncsr_local_group_8	0.125	0.05	6340
X-RAY DIFFRACTION	r_ncsr_local_group_9	0.117	0.05	6324
X-RAY DIFFRACTION	r_ncsr_local_group_10	0.125	0.05	6310
X-RAY DIFFRACTION	r_ncsr_local_group_11	0.094	0.05	12292
X-RAY DIFFRACTION	r_ncsr_local_group_12	0.131	0.05	6285

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Refine-ID	Type	Rms dev position (Å)	Weight position
1	1	A	X-RAY DIFFRACTION	Local ncs	0.08837	0.05008
1	2	B	X-RAY DIFFRACTION	Local ncs	0.08837	0.05008
2	3	A	X-RAY DIFFRACTION	Local ncs	0.08779	0.05008
2	4	E	X-RAY DIFFRACTION	Local ncs	0.08779	0.05008
3	5	A	X-RAY DIFFRACTION	Local ncs	0.09135	0.05008
3	6	F	X-RAY DIFFRACTION	Local ncs	0.09135	0.05008
4	7	B	X-RAY DIFFRACTION	Local ncs	0.08797	0.05008
4	8	E	X-RAY DIFFRACTION	Local ncs	0.08797	0.05008
5	9	B	X-RAY DIFFRACTION	Local ncs	0.09245	0.05008
5	10	F	X-RAY DIFFRACTION	Local ncs	0.09245	0.05008
6	11	C	X-RAY DIFFRACTION	Local ncs	0.1172	0.05007
6	12	D	X-RAY DIFFRACTION	Local ncs	0.1172	0.05007
7	13	C	X-RAY DIFFRACTION	Local ncs	0.12293	0.05007
7	14	G	X-RAY DIFFRACTION	Local ncs	0.12293	0.05007
8	15	C	X-RAY DIFFRACTION	Local ncs	0.12509	0.05007
8	16	H	X-RAY DIFFRACTION	Local ncs	0.12509	0.05007
9	17	D	X-RAY DIFFRACTION	Local ncs	0.11671	0.05007
9	18	G	X-RAY DIFFRACTION	Local ncs	0.11671	0.05007
10	19	D	X-RAY DIFFRACTION	Local ncs	0.12461	0.05007
10	20	H	X-RAY DIFFRACTION	Local ncs	0.12461	0.05007
11	21	E	X-RAY DIFFRACTION	Local ncs	0.09442	0.05008
11	22	F	X-RAY DIFFRACTION	Local ncs	0.09442	0.05008
12	23	G	X-RAY DIFFRACTION	Local ncs	0.13083	0.05007
12	24	H	X-RAY DIFFRACTION	Local ncs	0.13083	0.05007

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	R_factor all	Num. reflection all	Fsc free	Fsc work	% reflection obs (%)	WR_factor R_work
1.92-1.97	0.357	787	0.327	15190	0.328	16139	0.885	0.901	98.9962	0.331
1.97-2.024	0.319	785	0.285	14856	0.286	15779	0.911	0.924	99.1254	0.288
2.024-2.082	0.288	736	0.256	14402	0.258	15269	0.924	0.938	99.1421	0.258
2.082-2.146	0.28	757	0.232	13963	0.235	14843	0.935	0.95	99.1713	0.23
2.146-2.216	0.266	697	0.21	13604	0.213	14419	0.945	0.962	99.1816	0.205
2.216-2.294	0.243	689	0.193	13125	0.195	13934	0.959	0.969	99.1388	0.185
2.294-2.38	0.224	701	0.175	12600	0.177	13456	0.961	0.976	98.8481	0.165
2.38-2.477	0.221	633	0.177	12157	0.179	12923	0.966	0.977	98.9708	0.166
2.477-2.587	0.219	646	0.171	11633	0.173	12434	0.967	0.98	98.7534	0.16
2.587-2.713	0.225	641	0.16	11048	0.163	11802	0.967	0.983	99.0425	0.151
2.713-2.859	0.205	581	0.162	10646	0.165	11330	0.971	0.983	99.0909	0.156
2.859-3.032	0.228	545	0.166	10001	0.169	10654	0.966	0.982	98.9863	0.162
3.032-3.241	0.188	499	0.165	9415	0.166	10031	0.978	0.983	98.8336	0.165
3.241-3.499	0.226	451	0.172	8743	0.175	9339	0.97	0.984	98.4474	0.175
3.499-3.831	0.187	427	0.166	8107	0.167	8636	0.982	0.986	98.8189	0.174
3.831-4.28	0.172	376	0.136	7292	0.138	7747	0.982	0.989	98.9802	0.151
4.28-4.936	0.148	326	0.133	6484	0.134	6875	0.986	0.99	99.0545	0.156
4.936-6.03	0.182	262	0.16	5483	0.161	5788	0.983	0.987	99.2571	0.184
6.03-8.465	0.167	235	0.168	4235	0.168	4502	0.983	0.985	99.2892	0.2
8.465-49.186	0.156	139	0.168	2378	0.167	2540	0.984	0.981	99.0945	0.209

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