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- PDB-8u33: Crystal structure of KAI2 S95C mutant -

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Basic information

Entry
Database: PDB / ID: 8u33
TitleCrystal structure of KAI2 S95C mutant
ComponentsProbable esterase KAI2
KeywordsHYDROLASE / a b hydrolase / karrikin signalling / plant hormone receptor
Function / homology
Function and homology information


de-etiolation / response to karrikin / photomorphogenesis / hydrolase activity / nucleus / cytosol
Similarity search - Function
Alpha/beta hydrolase family / Alpha/beta hydrolase fold-1 / Alpha/Beta hydrolase fold
Similarity search - Domain/homology
Probable esterase KAI2
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.51 Å
AuthorsDavies, S.F. / Waters, M.T. / Bond, C.S.
Funding support Australia, 4items
OrganizationGrant numberCountry
Australian Research Council (ARC)FT150100162 Australia
Australian Research Council (ARC)LE120100092 Australia
Australian Research Council (ARC)LE140100096 Australia
Australian Research Council (ARC)LE170100199 Australia
CitationJournal: To Be Published
Title: Crystal structure of KAI2 S95C mutant
Authors: Davies, S.F. / Bond, C.S. / Waters, M.T.
History
DepositionSep 7, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 18, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Probable esterase KAI2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,6079
Polymers29,8801
Non-polymers7278
Water4,270237
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.798, 55.869, 53.147
Angle α, β, γ (deg.)90.00, 116.02, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Probable esterase KAI2 / Protein DWARF-14-like / Protein D14-like / Protein HYPOSENSITIVE TO LIGHT / Protein KARRIKIN INSENSITIVE 2


Mass: 29879.975 Da / Num. of mol.: 1 / Mutation: S95C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: KAI2, D14L, HTL, At4g37470, F6G17.120 / Plasmid: pSUMO / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2(DE3) / References: UniProt: Q9SZU7
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 237 / 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: 2.27 Å3/Da / Density % sol: 45.77 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: 2.2 M ammonium sulfate, 1 M HEPES pH 7.2; KAI2 protein at 14 mg/mL, 1mM dGR24^(ent-5DS) ligand in DMSO

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9464 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 10, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9464 Å / Relative weight: 1
ReflectionResolution: 1.51→47.76 Å / Num. obs: 41446 / % possible obs: 99.3 % / Redundancy: 6.9 % / CC1/2: 0.998 / Rmerge(I) obs: 0.118 / Rpim(I) all: 0.073 / Χ2: 0.54 / Net I/σ(I): 8.2
Reflection shellResolution: 1.51→1.54 Å / Redundancy: 6.5 % / Rmerge(I) obs: 1.353 / Mean I/σ(I) obs: 0.9 / Num. unique obs: 1790 / CC1/2: 0.466 / Rpim(I) all: 0.844 / Χ2: 0.47 / % possible all: 86.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0405refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.51→47.76 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.969 / SU B: 1.578 / SU ML: 0.055 / Cross valid method: THROUGHOUT / ESU R: 0.069 / ESU R Free: 0.071 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18622 2136 5.2 %RANDOM
Rwork0.15579 ---
obs0.15736 39292 99.28 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.061 Å2
Baniso -1Baniso -2Baniso -3
1-0.52 Å2-0 Å20.13 Å2
2---0.59 Å2-0 Å2
3----0.04 Å2
Refinement stepCycle: 1 / Resolution: 1.51→47.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2077 0 45 237 2359
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0122220
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162090
X-RAY DIFFRACTIONr_angle_refined_deg1.6831.6313025
X-RAY DIFFRACTIONr_angle_other_deg0.561.5684822
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5065283
X-RAY DIFFRACTIONr_dihedral_angle_2_deg5.221510
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.61310354
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0880.2352
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022567
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02489
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.8471.8151091
X-RAY DIFFRACTIONr_mcbond_other1.8391.8141091
X-RAY DIFFRACTIONr_mcangle_it2.8133.2581365
X-RAY DIFFRACTIONr_mcangle_other2.8183.261366
X-RAY DIFFRACTIONr_scbond_it3.6482.2221129
X-RAY DIFFRACTIONr_scbond_other3.6462.2231130
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.3713.8881653
X-RAY DIFFRACTIONr_long_range_B_refined6.34920.82548
X-RAY DIFFRACTIONr_long_range_B_other6.22218.772498
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.51→1.553 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.291 149 -
Rwork0.269 2624 -
obs--90.65 %

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