PDB-8v8n: Switchgrass Chalcone Synthase C170S

ID or keywords:

Entry

Database: PDB / ID: 8v8n

Title

Switchgrass Chalcone Synthase C170S

Components

Chalcone synthase

Keywords

TRANSFERASE / Chalcone Synthase / Flavonoids / Chalcones / Panicum Vigratum / switchgrass

Function / homology

Function and homology information

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

Biological species

Panicum virgatum (switchgrass)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.12 Å

Authors

Lewis, J.A. / Kang, C.

Funding support

United States, 2items

Citation

Journal: Int J Mol Sci / Year: 2024
Title: Structural and Interactional Analysis of the Flavonoid Pathway Proteins: Chalcone Synthase, Chalcone Isomerase and Chalcone Isomerase-like Protein.
Authors: Lewis, J.A. / Jacobo, E.P. / Palmer, N. / Vermerris, W. / Sattler, S.E. / Brozik, J.A. / Sarath, G. / Kang, C.

History

Deposition	Dec 5, 2023	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	May 29, 2024	Provider: repository / Type: Initial release
Revision 1.1	Jul 3, 2024	Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8v8n.cif.gz	165.5 KB	Display	PDBx/mmCIF format
PDB format	pdb8v8n.ent.gz	129.9 KB	Display	PDB format
PDBx/mmJSON format	8v8n.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8v8n_validation.pdf.gz	261.5 KB	Display	wwPDB validaton report
Full document	8v8n_full_validation.pdf.gz	261.5 KB	Display
Data in XML	8v8n_validation.xml.gz	1.2 KB	Display
Data in CIF	8v8n_validation.cif.gz	10.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/v8/8v8n ftp://data.pdbj.org/pub/pdb/validation_reports/v8/8v8n	HTTPS FTP

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Related structure data

Related structure data	8v8lC 8v8mC 8v8oC 8v8pC 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

hetero molecules

86.7 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	55.757, 61.722, 204.087
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Chalcone synthase Mass: 43300.574 Da / Num. of mol.: 2 / Mutation: C170S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Panicum virgatum (switchgrass) / Gene: PVAP13_8KG261900 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A8T0PQ54
#2: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C₃H₈O₃
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 382 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.05 Å³/Da / Density % sol: 39.97 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, hanging drop / Details: 0.2 M Potassium Sodium Tartrate, 20% PEG 3350

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

ALS

/ Beamline: 5.0.1 / Wavelength: 1 Å

Detector

Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Apr 16, 2022

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 1 Å / Relative weight: 1

Reflection

Resolution: 2.12→50 Å / Num. obs: 148323 / % possible obs: 95.3 % / Redundancy: 3.5 % / CC_1/2: 0.979 / CC star: 0.995 / R_merge(I) obs: 0.138 / R_pim(I) all: 0.085 / R_rim(I) all: 0.164 / Χ²: 0.556 / Net I/σ(I): 3.6

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique obs	CC_1/2	CC star	R_pim(I) all	R_rim(I) all	Χ²	% possible all
2.12-2.16	2.7	0.432	1528	0.824	0.951	0.28	0.519	0.453	77.7
2.16-2.2	2.9	0.468	1646	0.844	0.957	0.3	0.56	0.474	81.8
2.2-2.24	3.1	0.457	1736	0.442	0.783	0.297	0.549	0.545	86.9
2.24-2.28	3.2	0.458	1832	0.83	0.952	0.286	0.544	0.458	91.9
2.28-2.33	3.3	0.465	1877	0.802	0.943	0.291	0.552	0.464	94.1
2.33-2.39	3.5	0.471	1950	0.792	0.94	0.293	0.559	0.45	97.6
2.39-2.45	3.5	0.409	1972	0.848	0.958	0.255	0.485	0.435	97.7
2.45-2.51	3.6	0.39	1988	0.857	0.961	0.244	0.463	0.442	98.9
2.51-2.59	3.6	0.342	1981	0.846	0.957	0.217	0.408	0.506	99
2.59-2.67	3.3	0.31	2015	0.882	0.968	0.203	0.374	0.483	99.3
2.67-2.77	3.4	0.29	2013	0.893	0.971	0.187	0.347	0.501	99.3
2.77-2.88	3.7	0.259	1928	0.907	0.975	0.161	0.308	0.497	96.4
2.88-3.01	3.7	0.209	1944	0.928	0.981	0.131	0.249	0.528	96.4
3.01-3.17	3.9	0.167	2023	0.954	0.988	0.1	0.196	0.542	99.5
3.17-3.37	3.9	0.128	2012	0.977	0.994	0.076	0.149	0.575	99.5
3.37-3.62	3.8	0.098	2058	0.987	0.997	0.058	0.115	0.613	99.2
3.62-3.99	3.8	0.089	2028	0.983	0.996	0.053	0.104	0.712	98.7
3.99-4.57	3.6	0.064	2053	0.991	0.998	0.039	0.075	0.647	99.4
4.57-5.75	3.3	0.062	2066	0.988	0.997	0.039	0.074	0.684	98
5.75-50	3.7	0.064	2131	0.988	0.997	0.039	0.075	0.915	94.8

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Processing

Software

Name	Version	Classification
PHENIX	(1.20_4459: ???)	refinement
HKL-2000		data scaling
HKL-2000		data reduction
PHENIX		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.12→39.33 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 21.02 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2112	1999	5.03 %
R_work	0.2095	-	-
obs	0.2096	39715	97.64 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 2.12→39.33 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5932	0	6	382	6320

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.003	6053
X-RAY DIFFRACTION	f_angle_d	0.524	8205
X-RAY DIFFRACTION	f_dihedral_angle_d	17.073	2226
X-RAY DIFFRACTION	f_chiral_restr	0.04	936
X-RAY DIFFRACTION	f_plane_restr	0.004	1068

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
2.12-2.18	0.268	130	0.2973	2451	X-RAY DIFFRACTION	92
2.18-2.24	0.2736	136	0.2813	2571	X-RAY DIFFRACTION	94
2.24-2.3	0.2792	138	0.273	2596	X-RAY DIFFRACTION	96
2.3-2.38	0.3083	142	0.2793	2667	X-RAY DIFFRACTION	97
2.38-2.46	0.2603	141	0.2685	2662	X-RAY DIFFRACTION	98
2.46-2.56	0.2613	141	0.2494	2696	X-RAY DIFFRACTION	99
2.56-2.68	0.2626	144	0.2521	2716	X-RAY DIFFRACTION	99
2.68-2.82	0.2434	143	0.2472	2685	X-RAY DIFFRACTION	99
2.82-2.99	0.2471	139	0.2424	2620	X-RAY DIFFRACTION	96
2.99-3.22	0.2513	146	0.2174	2766	X-RAY DIFFRACTION	100
3.23-3.55	0.182	147	0.189	2754	X-RAY DIFFRACTION	100
3.55-4.06	0.1754	148	0.1695	2785	X-RAY DIFFRACTION	100
4.06-5.12	0.1509	150	0.1464	2832	X-RAY DIFFRACTION	100
5.12-39.33	0.1605	154	0.1769	2915	X-RAY DIFFRACTION	98

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