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- PDB-4hta: The structure of the karrikin insensitive (KAI2) protein in Arabi... -

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Basic information

Entry
Database: PDB / ID: 4hta
TitleThe structure of the karrikin insensitive (KAI2) protein in Arabidopsis thaliana
ComponentsHydrolase, alpha/beta fold family protein
KeywordsHYDROLASE / alpha/beta hydrolase / SIGNALING PROTEIN
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
PHOSPHATE ION / Probable esterase KAI2
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.901 Å
AuthorsBythell-Douglas, R. / Waters, M.T. / Scaffidi, A. / Flematti, G.R. / Smith, S.M. / Bond, C.S.
CitationJournal: Plos One / Year: 2013
Title: The Structure of the Karrikin-Insensitive Protein (KAI2) in Arabidopsis thaliana
Authors: Bythell-Douglas, R. / Waters, M.T. / Scaffidi, A. / Flematti, G.R. / Smith, S.M. / Bond, C.S.
History
DepositionNov 1, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 27, 2013Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hydrolase, alpha/beta fold family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,5287
Polymers31,9721
Non-polymers5556
Water4,792266
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)63.385, 66.064, 77.620
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Hydrolase, alpha/beta fold family protein / Karrikin-insensitive 2 / KAI2 / Putative uncharacterized protein AT4g37470 / Putative ...Karrikin-insensitive 2 / KAI2 / Putative uncharacterized protein AT4g37470 / Putative uncharacterized protein At4g37470 / Putative uncharacterized protein F6G17.120


Mass: 31972.303 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: F6G17.120, AT4G37470 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9SZU7
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 266 / 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: 2.54 Å3/Da / Density % sol: 51.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.2
Details: 1.5M sodium potassium phosphate, pH 7.2, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9539 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 2, 2012
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9539 Å / Relative weight: 1
ReflectionResolution: 1.901→77.62 Å / Num. all: 26147 / Num. obs: 26147 / % possible obs: 100 % / Biso Wilson estimate: 20.58 Å2
Reflection shellResolution: 1.9→2 Å / % possible all: 100

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
BUSTER2.10.0refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.901→50.31 Å / Cor.coef. Fo:Fc: 0.9531 / Cor.coef. Fo:Fc free: 0.9479 / Occupancy max: 1 / Occupancy min: 0.5 / SU R Cruickshank DPI: 0.113 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.122 / SU Rfree Blow DPI: 0.105 / SU Rfree Cruickshank DPI: 0.101 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.174 1324 5.07 %RANDOM
Rwork0.1552 ---
all0.1562 26093 --
obs0.1562 26093 99.11 %-
Displacement parametersBiso max: 92.78 Å2 / Biso mean: 22.48 Å2 / Biso min: 3.15 Å2
Baniso -1Baniso -2Baniso -3
1-0.3796 Å20 Å20 Å2
2--2.8596 Å20 Å2
3----3.2392 Å2
Refine analyzeLuzzati coordinate error obs: 0.159 Å
Refinement stepCycle: LAST / Resolution: 1.901→50.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2106 0 35 266 2407
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d736SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes56HARMONIC2
X-RAY DIFFRACTIONt_gen_planes313HARMONIC5
X-RAY DIFFRACTIONt_it2187HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion277SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact2788SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d2187HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg2968HARMONIC20.96
X-RAY DIFFRACTIONt_omega_torsion3.32
X-RAY DIFFRACTIONt_other_torsion15.45
LS refinement shellResolution: 1.9→1.98 Å / Total num. of bins used: 13
RfactorNum. reflection% reflection
Rfree0.2233 125 4.67 %
Rwork0.1827 2552 -
all0.1846 2677 -
obs--99.11 %

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