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- PDB-4ih1: Crystal structure of Karrikin Insensitive 2 (KAI2) from Arabidops... -

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Basic information

Entry
Database: PDB / ID: 4ih1
TitleCrystal structure of Karrikin Insensitive 2 (KAI2) from Arabidopsis thaliana
ComponentsHydrolase, alpha/beta fold family protein
KeywordsHYDROLASE / Karrikin receptor / 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: 1.55 Å
AuthorsZhou, X.E. / Zhao, L.-H. / Wu, Z.-S. / Yi, W. / Li, S. / Li, Y. / Xu, Y. / Xu, T.-H. / Liu, Y. / Chen, R.-Z. ...Zhou, X.E. / Zhao, L.-H. / Wu, Z.-S. / Yi, W. / Li, S. / Li, Y. / Xu, Y. / Xu, T.-H. / Liu, Y. / Chen, R.-Z. / Kovach, A. / Kang, Y. / Hou, L. / He, Y. / Zhang, C. / Melcher, K. / Xu, H.E.
CitationJournal: Cell Res. / Year: 2013
Title: Crystal structures of two phytohormone signal-transducing alpha / beta hydrolases: karrikin-signaling KAI2 and strigolactone-signaling DWARF14.
Authors: Zhao, L.H. / Zhou, X.E. / Wu, Z.S. / Yi, W. / Xu, Y. / Li, S. / Xu, T.H. / Liu, Y. / Chen, R.Z. / Kovach, A. / Kang, Y. / Hou, L. / He, Y. / Xie, C. / Song, W. / Zhong, D. / Xu, Y. / Wang, Y. ...Authors: Zhao, L.H. / Zhou, X.E. / Wu, Z.S. / Yi, W. / Xu, Y. / Li, S. / Xu, T.H. / Liu, Y. / Chen, R.Z. / Kovach, A. / Kang, Y. / Hou, L. / He, Y. / Xie, C. / Song, W. / Zhong, D. / Xu, Y. / Wang, Y. / Li, J. / Zhang, C. / Melcher, K. / Xu, H.E.
History
DepositionDec 18, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 30, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2013Group: Database references
Revision 1.2Sep 20, 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: Hydrolase, alpha/beta fold family protein


Theoretical massNumber of molelcules
Total (without water)29,8161
Polymers29,8161
Non-polymers00
Water2,054114
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)51.335, 56.013, 53.525
Angle α, β, γ (deg.)90.000, 116.150, 90.000
Int Tables number4
Space group name H-MP1211
Detailsbiological unit is the same as asym.

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Components

#1: Protein Hydrolase, alpha/beta fold family protein / Putative uncharacterized protein AT4g37470 / Putative uncharacterized protein At4g37470 / Putative ...Putative uncharacterized protein AT4g37470 / Putative uncharacterized protein At4g37470 / Putative uncharacterized protein F6G17.120


Mass: 29815.916 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: AT4g37470, F6G17.120, kai2 / Plasmid: pETDuet1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q9SZU7
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 114 / 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: 2.32 Å3/Da / Density % sol: 46.91 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 7.5
Details: PEG400, ammonium sulfate, pH 7.5, vapor diffusion, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Mar 21, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.55→30 Å / Num. all: 39492 / Num. obs: 39492 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 7.1 % / Rmerge(I) obs: 0.099 / Χ2: 1.093 / Net I/σ(I): 8.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.55-1.615.80.62639000.873199.6
1.61-1.676.70.5539310.8781100
1.67-1.757.10.46339360.9281100
1.75-1.847.40.34839200.9861100
1.84-1.957.50.2539301.0981100
1.95-2.17.50.17139441.2121100
2.1-2.327.50.11739631.1741100
2.32-2.657.50.08639501.1821100
2.65-3.347.50.06739661.1211100
3.34-306.90.07840521.396199.9

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
REFMAC5.5.0072refinement
PDB_EXTRACT3.11data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1WOM

1wom


Resolution: 1.55→30 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.963 / Occupancy max: 1 / Occupancy min: 1 / SU B: 1.385 / SU ML: 0.05 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.08 / ESU R Free: 0.075 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1927 2823 7.2 %RANDOM
Rwork0.1786 ---
obs0.1797 39469 99.78 %-
all-39635 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 66 Å2 / Biso mean: 24.3917 Å2 / Biso min: 11.93 Å2
Baniso -1Baniso -2Baniso -3
1-2.35 Å20 Å21.17 Å2
2---1.15 Å20 Å2
3----0.16 Å2
Refinement stepCycle: LAST / Resolution: 1.55→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2082 0 0 114 2196
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0222129
X-RAY DIFFRACTIONr_bond_other_d0.0010.021385
X-RAY DIFFRACTIONr_angle_refined_deg1.2721.9542899
X-RAY DIFFRACTIONr_angle_other_deg0.90333391
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0725267
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.35424.59298
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.57215341
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.3651510
X-RAY DIFFRACTIONr_chiral_restr0.0850.2332
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212389
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02423
X-RAY DIFFRACTIONr_mcbond_it0.9951.51333
X-RAY DIFFRACTIONr_mcbond_other0.2491.5541
X-RAY DIFFRACTIONr_mcangle_it1.82822166
X-RAY DIFFRACTIONr_scbond_it2.5853796
X-RAY DIFFRACTIONr_scangle_it4.2524.5733
LS refinement shellResolution: 1.551→1.591 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.262 197 -
Rwork0.24 2618 -
all-2815 -
obs--97.54 %

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