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- PDB-4hrx: Crystal structure of KAI2 -

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Basic information

Entry
Database: PDB / ID: 4hrx
TitleCrystal structure of KAI2
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
Probable esterase KAI2
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.11 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
DepositionOct 29, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 27, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 8, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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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)31,9721
Polymers31,9721
Non-polymers00
Water3,495194
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)50.199, 56.037, 52.425
Angle α, β, γ (deg.)90.00, 116.12, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Hydrolase, alpha/beta fold family protein / Karrikin-insensitive 2 / Putative uncharacterized protein AT4g37470 / Putative uncharacterized ...Karrikin-insensitive 2 / 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: AT4g37470, F6G17.120 / Plasmid: pDEST17 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta / References: UniProt: Q9SZU7
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 194 / 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: 2.07 Å3/Da / Density % sol: 40.6 %
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: 2.11→56.04 Å / Num. all: 15121 / Num. obs: 14659 / % possible obs: 97.1 % / Redundancy: 7.4 % / Biso Wilson estimate: 23.78 Å2 / Rmerge(I) obs: 0.162 / Net I/σ(I): 11.1
Reflection shellResolution: 2.11→2.23 Å / % possible all: 86.5

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
BUSTER2.10.0refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1WOM

1wom


Resolution: 2.11→47.07 Å / Cor.coef. Fo:Fc: 0.9386 / Cor.coef. Fo:Fc free: 0.9182 / Occupancy max: 1 / Occupancy min: 1 / SU R Cruickshank DPI: 0.218 / Cross valid method: THROUGHOUT / σ(F): 32 / SU R Blow DPI: 0.232 / SU Rfree Blow DPI: 0.175 / SU Rfree Cruickshank DPI: 0.173 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2063 739 5.05 %RANDOM
Rwork0.1609 ---
all0.1632 15121 --
obs0.1632 14645 96.49 %-
Displacement parametersBiso max: 85.23 Å2 / Biso mean: 22.19 Å2 / Biso min: 7.64 Å2
Baniso -1Baniso -2Baniso -3
1--5.4998 Å20 Å2-4.1167 Å2
2--4.9536 Å20 Å2
3---0.5462 Å2
Refine analyzeLuzzati coordinate error obs: 0.205 Å
Refinement stepCycle: LAST / Resolution: 2.11→47.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2070 0 0 194 2264
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d711SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes55HARMONIC2
X-RAY DIFFRACTIONt_gen_planes308HARMONIC5
X-RAY DIFFRACTIONt_it2117HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion275SEMIHARMONIC5
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_contact2677SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d2117HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg2884HARMONIC21.07
X-RAY DIFFRACTIONt_omega_torsion3.11
X-RAY DIFFRACTIONt_other_torsion17.63
LS refinement shellResolution: 2.11→2.28 Å / Total num. of bins used: 7
RfactorNum. reflection% reflection
Rfree0.2354 137 5.01 %
Rwork0.1857 2599 -
all0.1883 2736 -
obs--96.49 %

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