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- PDB-8v8l: Switchgrass Chalcone Isomerase -

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Basic information

Entry
Database: PDB / ID: 8v8l
TitleSwitchgrass Chalcone Isomerase
ComponentsChalcone-flavonone isomerase family protein
KeywordsISOMERASE / Chalcone Isomerase / Flavonoids / Chalcones / Panicum Vigratum / switchgrass
Function / homologyChalcone--flavonone isomerase / Chalcone-flavanone isomerase / Chalcone isomerase, orthogonal bundle domain superfamily / Chalcone isomerase, 3-layer sandwich / Chalcone isomerase / Chalcone isomerase superfamily / chalcone isomerase activity / flavonoid biosynthetic process / Chalcone-flavonone isomerase family protein
Function and homology information
Biological speciesPanicum virgatum (switchgrass)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.74 Å
AuthorsLewis, J.A. / Kang, C.
Funding support United States, 2items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)CHE-1804699 United States
National Science Foundation (NSF, United States)MCB-2043248 United States
CitationJournal: 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
DepositionDec 5, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 29, 2024Provider: repository / Type: Initial release
Revision 1.1Jul 3, 2024Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Chalcone-flavonone isomerase family protein
B: Chalcone-flavonone isomerase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,8934
Polymers48,7092
Non-polymers1842
Water4,702261
1
A: Chalcone-flavonone isomerase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,4472
Polymers24,3551
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Chalcone-flavonone isomerase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,4472
Polymers24,3551
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)139.090, 46.521, 59.054
Angle α, β, γ (deg.)90.00, 106.37, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Chalcone-flavonone isomerase family protein


Mass: 24354.596 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Panicum virgatum (switchgrass) / Gene: PVAP13_9KG390224 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A8T0N7A2
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 261 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.88 Å3/Da / Density % sol: 34.63 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: magnesium chloride, Tris-HCl, PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Nov 16, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.74→50 Å / Num. obs: 36980 / % possible obs: 98.2 % / Redundancy: 3.1 % / CC1/2: 0.99 / CC star: 0.997 / Rmerge(I) obs: 0.07 / Rpim(I) all: 0.046 / Rrim(I) all: 0.084 / Χ2: 0.914 / Net I/σ(I): 6.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2-2.032.30.5969990.6660.8940.4350.7420.45284.2
2.03-2.072.60.47610780.7480.9250.3380.5860.46789.3
2.07-2.112.70.43711470.7960.9420.3030.5340.44695.7
2.11-2.152.90.40211250.7760.9350.2760.490.47296.8
2.15-2.230.35312000.8570.9610.240.4290.47298.7
2.2-2.2530.31611770.8790.9670.2140.3830.75199.5
2.25-2.312.90.26311700.9010.9740.1820.3210.52999.5
2.31-2.3730.25111780.9260.9810.1710.3050.566100
2.37-2.443.10.20812100.950.9870.1410.2520.653100
2.44-2.523.30.19711880.9520.9880.1270.2350.59799.9
2.52-2.613.40.17212000.9620.990.1090.2040.607100
2.61-2.713.40.14211960.9750.9940.090.1690.695100
2.71-2.843.40.12111980.9790.9950.0780.1440.756100
2.84-2.993.30.09812170.9810.9950.0640.1170.791100
2.99-3.173.30.07911850.9910.9980.0510.0941.048100
3.17-3.4230.06112180.9930.9980.0420.0741.267100
3.42-3.763.20.05412000.9950.9990.0350.0641.47199.9
3.76-4.313.40.04812100.9960.9990.030.0571.60599.9
4.31-5.433.30.04612310.9950.9990.030.0551.60699.8
5.43-503.20.04512640.9960.9990.030.0542.18299.8

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Processing

Software
NameVersionClassification
PHENIX(1.20_4459: ???)refinement
HKL-2000data scaling
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.74→36.39 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.82 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2398 2000 5.41 %
Rwork0.196 --
obs0.1984 36980 98.02 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.74→36.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3127 0 12 261 3400
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063207
X-RAY DIFFRACTIONf_angle_d0.7414351
X-RAY DIFFRACTIONf_dihedral_angle_d5.532448
X-RAY DIFFRACTIONf_chiral_restr0.053494
X-RAY DIFFRACTIONf_plane_restr0.007564
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.74-1.780.31981370.28592385X-RAY DIFFRACTION95
1.78-1.830.31041420.26652494X-RAY DIFFRACTION98
1.83-1.880.29921400.26352457X-RAY DIFFRACTION97
1.88-1.940.30341410.24992465X-RAY DIFFRACTION97
1.94-2.010.28221390.23622423X-RAY DIFFRACTION96
2.01-2.090.31061440.21582514X-RAY DIFFRACTION99
2.09-2.190.2551440.21192529X-RAY DIFFRACTION99
2.19-2.30.2321430.19732504X-RAY DIFFRACTION99
2.3-2.450.24421460.19252535X-RAY DIFFRACTION99
2.45-2.640.23381410.19892481X-RAY DIFFRACTION99
2.64-2.90.25331430.20422493X-RAY DIFFRACTION97
2.9-3.320.24531450.19732543X-RAY DIFFRACTION100
3.32-4.180.20421470.16952569X-RAY DIFFRACTION99
4.18-36.390.21751480.17712588X-RAY DIFFRACTION98

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