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- PDB-8vcz: Crystal Structure of KAI2 from Oryza sativa -

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Basic information

Entry
Database: PDB / ID: 8vcz
TitleCrystal Structure of KAI2 from Oryza sativa
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: 1.68 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


Theoretical massNumber of molelcules
Total (without water)29,7471
Polymers29,7471
Non-polymers00
Water1,856103
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)37.636, 85.385, 44.620
Angle α, β, γ (deg.)90.00, 114.91, 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 103 / 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: 2.19 Å3/Da / Density % sol: 43.92 %
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: 8.2.1 / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Dec 1, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.68→42.73 Å / Num. obs: 27040 / % possible obs: 93.8 % / Redundancy: 3.5 % / Rsym value: 0.069 / Net I/σ(I): 16
Reflection shellResolution: 1.68→1.71 Å / Redundancy: 3.5 % / Num. unique obs: 1274 / Rsym value: 0.422 / % possible all: 84.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0411refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.68→42.73 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.956 / SU B: 2.343 / SU ML: 0.074 / Cross valid method: THROUGHOUT / ESU R: 0.105 / ESU R Free: 0.101 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1975 1428 5.3 %RANDOM
Rwork0.16791 ---
obs0.16949 25611 93.36 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.166 Å2
Baniso -1Baniso -2Baniso -3
1--0.18 Å2-0 Å20.14 Å2
2--2.69 Å20 Å2
3----1.84 Å2
Refinement stepCycle: 1 / Resolution: 1.68→42.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2067 0 0 103 2170
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0122116
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161988
X-RAY DIFFRACTIONr_angle_refined_deg1.5531.6332887
X-RAY DIFFRACTIONr_angle_other_deg0.5041.5664573
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6345270
X-RAY DIFFRACTIONr_dihedral_angle_2_deg4.231510
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.31910327
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0750.2337
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022457
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02463
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_it1.9192.0351083
X-RAY DIFFRACTIONr_mcbond_other1.9132.0351083
X-RAY DIFFRACTIONr_mcangle_it2.7513.651352
X-RAY DIFFRACTIONr_mcangle_other2.753.6531353
X-RAY DIFFRACTIONr_scbond_it3.1572.3891033
X-RAY DIFFRACTIONr_scbond_other3.1552.3911034
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.9094.2121536
X-RAY DIFFRACTIONr_long_range_B_refined5.90922.252375
X-RAY DIFFRACTIONr_long_range_B_other5.86821.652354
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.684→1.728 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.265 85 -
Rwork0.232 1757 -
obs--85.28 %

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