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- PDB-8vd1: Crystal Structure of KAI2 from Oryza sativa with MPD -

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Basic information

Entry
Database: PDB / ID: 8vd1
TitleCrystal Structure of KAI2 from Oryza sativa with MPD
ComponentsProbable esterase D14L
KeywordsHYDROLASE / Karrikin / signalling / alpha/beta-hydrolase / rice
Function / homologyarbuscular mycorrhizal association / response to karrikin / Alpha/beta hydrolase family / Alpha/beta hydrolase fold-1 / Alpha/Beta hydrolase fold / hydrolase activity / nucleus / cytoplasm / Probable esterase D14L
Function and homology information
Biological speciesOryza sativa (Asian cultivated rice)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.29 Å
AuthorsGilio, A.K. / Shabek, N. / Guercio, A.M. / Pawlak, J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States) United States
CitationJournal: J.Biol.Chem. / Year: 2024
Title: Structural insights into rice KAI2 receptor provide functional implications for perception and signal transduction.
Authors: Guercio, A.M. / Gilio, A.K. / Pawlak, J. / Shabek, N.
History
DepositionDec 14, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 31, 2024Provider: repository / Type: Initial release
Revision 1.1Aug 7, 2024Group: Database references / Category: citation
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Aug 21, 2024Group: Database references / Category: citation / Item: _citation.journal_volume

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Probable esterase D14L
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,8652
Polymers29,7471
Non-polymers1181
Water4,378243
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)37.711, 86.477, 44.617
Angle α, β, γ (deg.)90.00, 114.94, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Probable esterase D14L / Protein DWARF-14-like / Protein D14-like / Protein HEBIBA D14L


Mass: 29746.975 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryza sativa (Asian cultivated rice) / Gene: D14L, Os03g0437600, LOC_Os03g32270, Os11g0384789 / Production host: Escherichia coli (E. coli) / References: UniProt: Q10J20
#2: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 243 / 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: 2.23 Å3/Da / Density % sol: 44.72 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M Sodium HEPES, 0.1M MOPS (acid) pH 7.5, 0.018M Magnesium chloride hexahydrate, 0.018M Calcium chloride dihydrate, 9.4% v/v MPD, 9.4% v/v PEG 1000, 9.4% v/v PEG 3350

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Data collection

DiffractionMean temperature: 298 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.999992 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: May 24, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999992 Å / Relative weight: 1
ReflectionResolution: 1.29→40.49 Å / Num. obs: 64764 / % possible obs: 99.3 % / Redundancy: 4.3 % / Rsym value: 0.051 / Net I/σ(I): 19.7
Reflection shellResolution: 1.29→1.31 Å / Num. unique obs: 2848 / Rsym value: 0.32

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Processing

Software
NameVersionClassification
REFMAC5.8.0411refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.29→40.49 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.97 / SU B: 0.678 / SU ML: 0.029 / Cross valid method: THROUGHOUT / ESU R: 0.043 / ESU R Free: 0.043 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.16812 3293 5.1 %RANDOM
Rwork0.15221 ---
obs0.15304 61470 99.34 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 13.478 Å2
Baniso -1Baniso -2Baniso -3
1--0.92 Å2-0 Å2-0.4 Å2
2--1.45 Å2-0 Å2
3----0.11 Å2
Refinement stepCycle: 1 / Resolution: 1.29→40.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2087 0 8 243 2338
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0122167
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162043
X-RAY DIFFRACTIONr_angle_refined_deg1.9251.6352959
X-RAY DIFFRACTIONr_angle_other_deg0.5781.5664705
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8435276
X-RAY DIFFRACTIONr_dihedral_angle_2_deg19.53511
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.9610341
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0950.2343
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.022528
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02476
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_it1.2611.3031098
X-RAY DIFFRACTIONr_mcbond_other1.2611.3031098
X-RAY DIFFRACTIONr_mcangle_it1.8222.3411376
X-RAY DIFFRACTIONr_mcangle_other1.8272.3431377
X-RAY DIFFRACTIONr_scbond_it2.5491.541069
X-RAY DIFFRACTIONr_scbond_other2.5481.541070
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.7822.7151584
X-RAY DIFFRACTIONr_long_range_B_refined4.53816.712530
X-RAY DIFFRACTIONr_long_range_B_other4.39715.062471
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.29→1.323 Å
RfactorNum. reflection% reflection
Rfree0.247 230 -
Rwork0.228 4173 -
obs--91.81 %

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