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- PDB-8dlc: Crystal structure of chalcone-isomerase like protein from Vitis v... -

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Basic information

Entry
Database: PDB / ID: 8dlc
TitleCrystal structure of chalcone-isomerase like protein from Vitis vinifera (VvCHIL)
ComponentsChalcone-flavonone isomerase family protein
KeywordsSIGNALING PROTEIN / Chalcone isomerase-fold
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 speciesVitis vinifera (wine grape)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsWolf Saxon, E. / Moorman, C. / Castro, A. / Ruiz, A. / Mallari, J.P. / Burke, J.R.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J.Biol.Chem. / Year: 2023
Title: Regulatory ligand binding in plant chalcone isomerase-like (CHIL) proteins.
Authors: Wolf-Saxon, E.R. / Moorman, C.C. / Castro, A. / Ruiz-Rivera, A. / Mallari, J.P. / Burke, J.R.
History
DepositionJul 7, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 10, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Nov 22, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Chalcone-flavonone isomerase family protein


Theoretical massNumber of molelcules
Total (without water)24,0411
Polymers24,0411
Non-polymers00
Water2,540141
1
A: Chalcone-flavonone isomerase family protein

A: Chalcone-flavonone isomerase family protein


Theoretical massNumber of molelcules
Total (without water)48,0832
Polymers48,0832
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+1/31
Buried area1360 Å2
ΔGint-13 kcal/mol
Surface area20020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.420, 49.420, 170.851
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Space group name HallP322"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: x-y,-y,-z+1/3
#5: -x,-x+y,-z+2/3
#6: y,x,-z
Components on special symmetry positions
IDModelComponents
11A-400-

HOH

DetailsThe dimer observed crystallographically has not been proven to represent the true biological inter-subunit interaction; however, it has been shown that the protein is dimeric.

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Components

#1: Protein Chalcone-flavonone isomerase family protein


Mass: 24041.383 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vitis vinifera (wine grape) / Gene: CHI3_0, CK203_016634 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A438J2L0
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 141 / Source method: isolated from a natural source / Formula: H2O

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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: 2.55 Å3/Da / Density % sol: 51.85 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / Details: 20% (w/v) PEG 3350 and 200 mM potassium nitrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 24, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→42.8 Å / Num. obs: 19994 / % possible obs: 100 % / Redundancy: 15.8 % / Biso Wilson estimate: 22.51 Å2 / Rmerge(I) obs: 0.19 / Rpim(I) all: 0.05 / Net I/σ(I): 10.7
Reflection shellResolution: 1.9→2 Å / Mean I/σ(I) obs: 2.2 / Num. unique obs: 2818 / Rpim(I) all: 0.439

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
Cootmodel building
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4dok

4dok


Resolution: 1.9→42.8 Å / SU ML: 0.2683 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 24.9878
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.237 1982 10.01 %
Rwork0.2011 17818 -
obs0.2047 19800 99.32 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 27.75 Å2
Refinement stepCycle: LAST / Resolution: 1.9→42.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1636 0 0 141 1777
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01091700
X-RAY DIFFRACTIONf_angle_d1.10352304
X-RAY DIFFRACTIONf_chiral_restr0.0682263
X-RAY DIFFRACTIONf_plane_restr0.0082294
X-RAY DIFFRACTIONf_dihedral_angle_d19.6526633
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.950.48781380.50251189X-RAY DIFFRACTION97.07
1.95-20.27381360.25281259X-RAY DIFFRACTION100
2-2.060.22411410.21061277X-RAY DIFFRACTION100
2.06-2.130.2761390.23231226X-RAY DIFFRACTION99.93
2.13-2.20.20491360.19211264X-RAY DIFFRACTION100
2.2-2.290.41321290.30821192X-RAY DIFFRACTION93.89
2.29-2.390.21471410.181256X-RAY DIFFRACTION100
2.39-2.520.22991460.19371281X-RAY DIFFRACTION100
2.52-2.680.2111430.19781266X-RAY DIFFRACTION100
2.68-2.880.25441430.19641274X-RAY DIFFRACTION100
2.88-3.170.2161440.1841282X-RAY DIFFRACTION100
3.18-3.630.21321460.17161312X-RAY DIFFRACTION99.73
3.63-4.580.18021450.15261315X-RAY DIFFRACTION99.79
4.58-42.80.23211550.19441425X-RAY DIFFRACTION99.87
Refinement TLS params.Method: refined / Origin x: 23.9152614717 Å / Origin y: -13.7142768208 Å / Origin z: 12.5134712215 Å
111213212223313233
T0.156147027679 Å20.00316426947134 Å20.00579988198479 Å2-0.134635278383 Å2-0.00570960490585 Å2--0.150813996248 Å2
L1.04006872096 °20.209476266215 °20.363934960785 °2-1.41948471242 °2-0.358491331476 °2--1.26634010829 °2
S-0.0142484522808 Å °-0.0200041802699 Å °0.0138171415185 Å °0.0484622382112 Å °0.0162208661259 Å °0.00630122437373 Å °-0.00576400923117 Å °0.0160150183043 Å °-0.00211410003604 Å °
Refinement TLS groupSelection details: all

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