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- PDB-5z9h: Crystal structure of KAI2_ply2(A219V) -

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Basic information

Entry
Database: PDB / ID: 5z9h
TitleCrystal structure of KAI2_ply2(A219V)
ComponentsProbable esterase KAI2
KeywordsHYDROLASE / alpha/beta hydrolase
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, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Probable esterase KAI2
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.49 Å
AuthorsKim, K.L. / Cha, J.S. / Soh, M.S. / Cho, H.S.
CitationJournal: J. Exp. Bot. / Year: 2018
Title: A missense allele of KARRIKIN-INSENSITIVE2 impairs ligand-binding and downstream signaling in Arabidopsis thaliana.
Authors: Lee, I. / Kim, K. / Lee, S. / Lee, S. / Hwang, E. / Shin, K. / Kim, D. / Choi, J. / Choi, H. / Cha, J.S. / Kim, H. / Lee, R.A. / Jeong, S. / Kim, J. / Kim, Y. / Nam, H.G. / Park, S.K. / Cho, H.S. / Soh, M.S.
History
DepositionFeb 3, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 22, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Probable esterase KAI2


Theoretical massNumber of molelcules
Total (without water)29,8441
Polymers29,8441
Non-polymers00
Water3,567198
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area11170 Å2
Unit cell
Length a, b, c (Å)50.842, 55.494, 53.019
Angle α, β, γ (deg.)90.00, 116.42, 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: 29843.967 Da / Num. of mol.: 1 / Mutation: A219V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: KAI2, D14L, HTL, At4g37470, F6G17.120 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9SZU7
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 198 / 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: 2.24 Å3/Da / Density % sol: 45.2 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / Details: 1M Na-citrate, 100 mM HEPES (pH 7.5), 5% glycerol

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Data collection

DiffractionMean temperature: 93.1 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.987 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Mar 14, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 1.49→50 Å / Num. obs: 43147 / % possible obs: 99.6 % / Redundancy: 6.4 % / Net I/σ(I): 48.75
Reflection shellResolution: 1.49→1.52 Å

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1WOM

1wom


Resolution: 1.49→27.747 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 2.22 / Phase error: 14.02
RfactorNum. reflection% reflection
Rfree0.168 2170 5.04 %
Rwork0.1341 --
obs0.1358 43059 99.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.49→27.747 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2073 0 0 198 2271
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062120
X-RAY DIFFRACTIONf_angle_d1.0282889
X-RAY DIFFRACTIONf_dihedral_angle_d12.94758
X-RAY DIFFRACTIONf_chiral_restr0.041332
X-RAY DIFFRACTIONf_plane_restr0.005377
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.49-1.52240.18371390.10992506X-RAY DIFFRACTION99
1.5224-1.55780.16661400.09762540X-RAY DIFFRACTION99
1.5578-1.59680.16131220.0942537X-RAY DIFFRACTION99
1.5968-1.63990.16241270.09442554X-RAY DIFFRACTION99
1.6399-1.68820.1411430.09412507X-RAY DIFFRACTION100
1.6882-1.74270.16881280.1032549X-RAY DIFFRACTION99
1.7427-1.8050.1611200.10962563X-RAY DIFFRACTION100
1.805-1.87720.15791250.11382578X-RAY DIFFRACTION100
1.8772-1.96260.15261280.11632576X-RAY DIFFRACTION100
1.9626-2.06610.16131260.11952534X-RAY DIFFRACTION100
2.0661-2.19550.16071420.12812569X-RAY DIFFRACTION100
2.1955-2.36490.17331530.13732529X-RAY DIFFRACTION100
2.3649-2.60270.17291220.14652597X-RAY DIFFRACTION100
2.6027-2.9790.18511450.16772565X-RAY DIFFRACTION100
2.979-3.75170.18811500.15912573X-RAY DIFFRACTION100
3.7517-27.75180.15711600.15392612X-RAY DIFFRACTION99

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