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- PDB-8v8p: Sorghum Chalcone Isomerase -

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Basic information

Entry
Database: PDB / ID: 8v8p
TitleSorghum Chalcone Isomerase
ComponentsChalcone-flavonone isomerase family protein
KeywordsISOMERASE / Chalcone Synthase / Flavonoids / Chalcones
Function / homology
Function and homology information


chalcone isomerase activity / flavonoid biosynthetic process
Similarity search - Function
Chalcone--flavonone isomerase / Chalcone-flavanone isomerase / Chalcone isomerase, orthogonal bundle domain superfamily / Chalcone isomerase, 3-layer sandwich / Chalcone isomerase / Chalcone isomerase superfamily
Similarity search - Domain/homology
7-HYDROXY-2-(4-HYDROXY-PHENYL)-CHROMAN-4-ONE / Chalcone-flavonone isomerase family protein
Similarity search - Component
Biological speciesSorghum bicolor (sorghum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.18 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
C: Chalcone-flavonone isomerase family protein
D: Chalcone-flavonone isomerase family protein
E: Chalcone-flavonone isomerase family protein
F: Chalcone-flavonone isomerase family protein
G: Chalcone-flavonone isomerase family protein
H: Chalcone-flavonone isomerase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)191,85013
Polymers190,5698
Non-polymers1,2815
Water00
1
A: Chalcone-flavonone isomerase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,3343
Polymers23,8211
Non-polymers5132
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Chalcone-flavonone isomerase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,0772
Polymers23,8211
Non-polymers2561
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Chalcone-flavonone isomerase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,0772
Polymers23,8211
Non-polymers2561
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Chalcone-flavonone isomerase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,0772
Polymers23,8211
Non-polymers2561
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Chalcone-flavonone isomerase family protein


Theoretical massNumber of molelcules
Total (without water)23,8211
Polymers23,8211
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Chalcone-flavonone isomerase family protein


Theoretical massNumber of molelcules
Total (without water)23,8211
Polymers23,8211
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
G: Chalcone-flavonone isomerase family protein


Theoretical massNumber of molelcules
Total (without water)23,8211
Polymers23,8211
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
H: Chalcone-flavonone isomerase family protein


Theoretical massNumber of molelcules
Total (without water)23,8211
Polymers23,8211
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)92.453, 127.825, 95.311
Angle α, β, γ (deg.)90.00, 116.27, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Chalcone-flavonone isomerase family protein


Mass: 23821.078 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sorghum bicolor (sorghum) / Gene: SORBI_3001G035600 / Production host: Escherichia coli (E. coli) / References: UniProt: C5WV22
#2: Chemical
ChemComp-DFV / 7-HYDROXY-2-(4-HYDROXY-PHENYL)-CHROMAN-4-ONE / 5-DEOXYFLAVANONE


Mass: 256.253 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C15H12O4 / Feature type: SUBJECT OF INVESTIGATION / Comment: agonist*YM
Has ligand of interestY

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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: 2.88 Å3/Da / Density % sol: 57.34 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: 25% PEG 1500

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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: Dec 22, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.18→50 Å / Num. obs: 33493 / % possible obs: 99.9 % / Redundancy: 3.4 % / CC1/2: 0.951 / CC star: 0.987 / Rmerge(I) obs: 0.197 / Rpim(I) all: 0.126 / Rrim(I) all: 0.235 / Χ2: 0.647 / Net I/σ(I): 3.1 / Num. measured all: 112827
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
3.18-3.233.10.60516360.590.8620.4040.730.55899.5
3.23-3.292.90.58616780.630.8790.4160.7220.52100
3.29-3.363.10.49216360.7350.920.3410.6010.523100
3.36-3.433.20.52217060.7640.9310.3430.6270.59399.9
3.43-3.53.30.38416370.7910.940.2480.4580.597100
3.5-3.583.10.31816800.8430.9560.2160.3860.55699.9
3.58-3.673.20.30716760.7540.9270.2060.3710.73100
3.67-3.773.60.30416460.8430.9560.1860.3570.736100
3.77-3.883.60.27816880.920.9790.1690.3260.555100
3.88-4.013.60.24216780.9490.9870.1480.2840.599100
4.01-4.153.60.19716700.9570.9890.1210.2320.54199.9
4.15-4.323.60.18616740.9630.990.1140.2180.63599.9
4.32-4.513.60.18716680.9510.9870.1130.2191.10699.9
4.51-4.753.50.13916750.980.9950.0860.1640.60799.9
4.75-5.053.50.1316670.9860.9960.0810.1540.5799.8
5.05-5.443.40.14416750.9770.9940.0920.1720.5299.9
5.44-5.983.20.14916800.9720.9930.0990.1790.505100
5.98-6.853.20.12216950.9780.9940.0820.1470.564100
6.85-8.623.40.07516940.9930.9980.0480.0890.596100
8.62-503.70.0617340.9930.9980.0360.071.14799.8

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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: 3.18→46.2 Å / SU ML: 0.43 / Cross valid method: FREE R-VALUE / σ(F): 0.11 / Phase error: 27.33 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2738 1881 6.1 %
Rwork0.2167 --
obs0.2202 30858 91.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.18→46.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12346 0 95 0 12441
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00212731
X-RAY DIFFRACTIONf_angle_d0.60517306
X-RAY DIFFRACTIONf_dihedral_angle_d15.344398
X-RAY DIFFRACTIONf_chiral_restr0.0411995
X-RAY DIFFRACTIONf_plane_restr0.0042219
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.18-3.260.3741340.31051982X-RAY DIFFRACTION83
3.26-3.360.35091200.28332037X-RAY DIFFRACTION84
3.36-3.470.32061340.26192147X-RAY DIFFRACTION88
3.47-3.590.32771390.25322212X-RAY DIFFRACTION92
3.59-3.730.3181590.25542306X-RAY DIFFRACTION96
3.74-3.90.27311390.22452212X-RAY DIFFRACTION92
3.91-4.110.28941350.2092212X-RAY DIFFRACTION91
4.11-4.370.21421630.19672271X-RAY DIFFRACTION94
4.37-4.70.27771400.18382270X-RAY DIFFRACTION94
4.71-5.180.26291420.19072279X-RAY DIFFRACTION94
5.18-5.930.29871530.21632270X-RAY DIFFRACTION93
5.93-7.460.2781570.20682333X-RAY DIFFRACTION96
7.46-46.20.17931660.15762446X-RAY DIFFRACTION99

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