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- PDB-8v8o: Switchgrass Chalcone Isomerase-Like Protein -

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Basic information

Entry
Database: PDB / ID: 8v8o
TitleSwitchgrass Chalcone Isomerase-Like Protein
ComponentsChalcone-flavonone isomerase family protein
KeywordsPROTEIN BINDING / Chalcone Synthase / Flavonoids / TRANSFERASE
Function / homologyChalcone--flavonone isomerase 3-like / intramolecular lyase activity / Chalcone-flavanone isomerase / Chalcone isomerase, orthogonal bundle domain superfamily / Chalcone isomerase / Chalcone isomerase, 3-layer sandwich / Chalcone isomerase superfamily / Chalcone-flavonone isomerase family protein
Function and homology information
Biological speciesPanicum virgatum (switchgrass)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.21 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)48,5672
Polymers48,5672
Non-polymers00
Water00
1
A: Chalcone-flavonone isomerase family protein


Theoretical massNumber of molelcules
Total (without water)24,2831
Polymers24,2831
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Chalcone-flavonone isomerase family protein


Theoretical massNumber of molelcules
Total (without water)24,2831
Polymers24,2831
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)100.171, 100.171, 118.930
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Chalcone-flavonone isomerase family protein


Mass: 24283.312 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Panicum virgatum (switchgrass) / Gene: PVAP13_8KG022400 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A8T0PCS1

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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: 3.07 Å3/Da / Density % sol: 59.95 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: 1.1 M Ammonium Tartrate Dibasic pH=7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Jun 8, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 12646 / % possible obs: 99.7 % / Redundancy: 12.4 % / CC1/2: 0.971 / CC star: 0.993 / Rpim(I) all: 0.108 / Rrim(I) all: 0.387 / Χ2: 0.549 / Net I/σ(I): 1.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Num. unique obsCC1/2CC starRpim(I) allΧ2% possible all
3-3.0510.86260.4660.7970.7060.447100
3.05-3.1111.76180.5220.8280.5570.443100
3.11-3.1712.36190.6550.890.5640.453100
3.17-3.2312.36180.6060.8690.3890.464100
3.23-3.311.96240.6590.8910.350.499100
3.3-3.3810.96170.6240.8770.290.554100
3.38-3.4610.55890.8070.9450.2680.51397.2
3.46-3.5612.56290.8620.9620.2290.561100
3.56-3.6613.96080.9350.9830.1540.531100
3.66-3.7813.76270.9390.9840.130.624100
3.78-3.9113.66280.9610.990.1240.491100
3.91-4.0713.56320.980.9950.1010.471100
4.07-4.2613.46310.9860.9970.0910.54100
4.26-4.4813.56260.9830.9960.0740.82100
4.48-4.7613.16480.9890.9970.0630.539100
4.76-5.1312.86310.990.9970.0560.479100
5.13-5.6412.26470.9890.9970.0660.489100
5.64-6.4611.26520.9810.9950.0730.499100
6.46-8.1312.36440.9940.9980.0420.59396.4
8.13-5012.47320.9970.9990.0260.8799.7

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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: 3.21→45.54 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 22.63 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2542 1027 10.01 %
Rwork0.2407 --
obs0.2421 10264 98.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.21→45.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3234 0 0 0 3234
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033300
X-RAY DIFFRACTIONf_angle_d0.5874468
X-RAY DIFFRACTIONf_dihedral_angle_d18.4431176
X-RAY DIFFRACTIONf_chiral_restr0.046510
X-RAY DIFFRACTIONf_plane_restr0.003572
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.21-3.380.32321440.30881298X-RAY DIFFRACTION99
3.38-3.590.30341400.27981261X-RAY DIFFRACTION97
3.59-3.870.25491450.26821306X-RAY DIFFRACTION100
3.87-4.260.23361460.24571307X-RAY DIFFRACTION99
4.26-4.870.23061470.20861324X-RAY DIFFRACTION99
4.87-6.140.25011480.2331332X-RAY DIFFRACTION99
6.14-45.540.2451570.20571409X-RAY DIFFRACTION98

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