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- PDB-8u2l: Crystal structure of KAI2 S95C L48I mutant -

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Basic information

Entry
Database: PDB / ID: 8u2l
TitleCrystal structure of KAI2 S95C L48I mutant
ComponentsKARRIKIN INSENSITIVE 2
KeywordsHYDROLASE / 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: 2.04 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 L48I mutant
Authors: Davies, S.F. / Bond, C.S. / Waters, M.T.
History
DepositionSep 6, 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: KARRIKIN INSENSITIVE 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,5378
Polymers29,8801
Non-polymers6577
Water1,69394
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.379, 55.676, 53.031
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 KARRIKIN INSENSITIVE 2 / 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, L48I
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.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 94 / 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: 2.28 Å3/Da / Density % sol: 46.16 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.7
Details: 2.2 M ammonium sulfate, 1 M HEPES pH 6.7; KAI2 protein at 13 mg/mL

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 10, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.04→47.66 Å / Num. obs: 16684 / % possible obs: 98.4 % / Redundancy: 6.1 % / CC1/2: 0.986 / Rmerge(I) obs: 0.2 / Rpim(I) all: 0.145 / Χ2: 0.92 / Net I/σ(I): 3.8
Reflection shellResolution: 2.04→2.09 Å / Redundancy: 5.3 % / Rmerge(I) obs: 1.201 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 1005 / CC1/2: 0.41 / Rpim(I) all: 0.822 / Χ2: 1.01 / % possible all: 80

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Processing

Software
NameVersionClassification
REFMAC5.8.0405refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.04→47.66 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.945 / SU B: 7.096 / SU ML: 0.18 / Cross valid method: THROUGHOUT / ESU R: 0.215 / ESU R Free: 0.182 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23336 890 5.3 %RANDOM
Rwork0.18247 ---
obs0.18521 15780 98.45 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.658 Å2
Baniso -1Baniso -2Baniso -3
1-0.97 Å20 Å20.66 Å2
2---1.23 Å20 Å2
3----0.26 Å2
Refinement stepCycle: 1 / Resolution: 2.04→47.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2077 0 39 94 2210
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0122155
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162007
X-RAY DIFFRACTIONr_angle_refined_deg1.4571.6322927
X-RAY DIFFRACTIONr_angle_other_deg0.4891.5694619
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8765264
X-RAY DIFFRACTIONr_dihedral_angle_2_deg6.669510
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.62410337
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0680.2339
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022470
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02474
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_it2.6673.2561066
X-RAY DIFFRACTIONr_mcbond_other2.6673.2561066
X-RAY DIFFRACTIONr_mcangle_it3.6245.8441326
X-RAY DIFFRACTIONr_mcangle_other3.6235.8451327
X-RAY DIFFRACTIONr_scbond_it4.1793.7881089
X-RAY DIFFRACTIONr_scbond_other4.1783.7891090
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.2436.7331602
X-RAY DIFFRACTIONr_long_range_B_refined7.45432.122498
X-RAY DIFFRACTIONr_long_range_B_other7.45332.132499
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.04→2.093 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.358 63 -
Rwork0.297 948 -
obs--81.34 %

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