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- PDB-5z9g: Crystal structure of KAI2 -

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Basic information

Entry
Database: PDB / ID: 5z9g
TitleCrystal structure of KAI2
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)29,8161
Polymers29,8161
Non-polymers00
Water4,125229
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area11390 Å2
Unit cell
Length a, b, c (Å)50.599, 55.785, 53.034
Angle α, β, γ (deg.)90.00, 116.07, 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: 29815.916 Da / Num. of mol.: 1
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.: 229 / 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: 2.25 Å3/Da / Density % sol: 45.45 %
Crystal growTemperature: 290 K / Method: vapor diffusion / pH: 7.5 / Details: 1M Na-citrate, 100 mM HEPES (pH 7.5), 5% glycerol

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Data collection

DiffractionMean temperature: 93.1 K / Ambient temp details: liquid nitrogen stream
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.987 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Mar 1, 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: 43387 / % possible obs: 99.7 % / Redundancy: 6.1 % / Net I/σ(I): 54.1
Reflection shellResolution: 1.49→1.52 Å

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Processing

Software
NameVersionClassification
REFMAC5.5.0110refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1WOM

1wom


Resolution: 1.49→47.64 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.954 / SU B: 1.801 / SU ML: 0.032 / Cross valid method: THROUGHOUT / ESU R: 0.069 / ESU R Free: 0.063 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17662 2183 5 %RANDOM
Rwork0.13647 ---
obs0.13854 41150 99.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 9.743 Å2
Baniso -1Baniso -2Baniso -3
1-0.78 Å20 Å20.29 Å2
2---0.55 Å20 Å2
3---0.02 Å2
Refinement stepCycle: 1 / Resolution: 1.49→47.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2066 0 0 229 2295
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0222112
X-RAY DIFFRACTIONr_bond_other_d0.0020.021368
X-RAY DIFFRACTIONr_angle_refined_deg1.9291.9532878
X-RAY DIFFRACTIONr_angle_other_deg1.1433351
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7785266
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.56524.63997
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.47215335
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.6881510
X-RAY DIFFRACTIONr_chiral_restr0.1590.2331
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0212375
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02417
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_it2.1331.51329
X-RAY DIFFRACTIONr_mcbond_other0.9741.5538
X-RAY DIFFRACTIONr_mcangle_it2.97622158
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.6113783
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it6.2924.5720
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr2.31433480
X-RAY DIFFRACTIONr_sphericity_free10.6533229
X-RAY DIFFRACTIONr_sphericity_bonded4.05733434
LS refinement shellResolution: 1.488→1.526 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.176 130 -
Rwork0.127 2936 -
obs--96.72 %

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