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- PDB-4jym: crystal Structure of KAI2 in complex with 3-methyl-2H-furo[2,3-c]... -

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Basic information

Entry
Database: PDB / ID: 4jym
Titlecrystal Structure of KAI2 in complex with 3-methyl-2H-furo[2,3-c]pyran-2-one
ComponentsHydrolase, alpha/beta fold family protein
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
3-methyl-2H-furo[2,3-c]pyran-2-one / Probable esterase KAI2
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.35 Å
AuthorsGuo, Y. / Zheng, Z. / Noel, J.P.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2013
Title: Smoke-derived karrikin perception by the alpha/beta-hydrolase KAI2 from Arabidopsis.
Authors: Guo, Y. / Zheng, Z. / La Clair, J.J. / Chory, J. / Noel, J.P.
History
DepositionMar 30, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 8, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2013Group: Database references
Revision 1.2Aug 28, 2019Group: Advisory / Data collection ...Advisory / Data collection / Refinement description / Structure summary
Category: chem_comp / pdbx_distant_solvent_atoms ...chem_comp / pdbx_distant_solvent_atoms / refine / reflns
Item: _chem_comp.pdbx_synonyms / _refine.ls_number_reflns_obs / _reflns.number_all
Revision 1.3Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)59,9324
Polymers59,6322
Non-polymers3002
Water11,530640
1
A: Hydrolase, alpha/beta fold family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,9662
Polymers29,8161
Non-polymers1501
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Hydrolase, alpha/beta fold family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,9662
Polymers29,8161
Non-polymers1501
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)50.950, 53.200, 55.760
Angle α, β, γ (deg.)90.040, 90.040, 116.030
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Hydrolase, alpha/beta fold family protein / KAI2


Mass: 29815.916 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: F6G17.120, AT4g37470, At4g37470, AT4G37470 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9SZU7
#2: Chemical ChemComp-KKN / 3-methyl-2H-furo[2,3-c]pyran-2-one / Karrikin KAR1


Mass: 150.131 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H6O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 640 / 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: 2.28 Å3/Da / Density % sol: 45.99 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 22% (w/v) polyethylene glycol 8000, 0.1 M Na+-PIPES (pH 6.5), 0.3 M NaBr and 2 mM DTT, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 28, 2012 / Details: mirror
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.35→26.487 Å / Num. obs: 99300 / % possible obs: 85.9 % / Redundancy: 2.4 % / Rsym value: 0.122 / Net I/σ(I): 4.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.35-1.421.10.4131.4931986660.41351.3
1.42-1.511.40.562117824129320.56280.7
1.51-1.611.80.3581.424291134980.35890.2
1.61-1.741.90.2272.324581129700.22792.6
1.74-1.912.20.2232.126736120440.22393.7
1.91-2.1330.216232642110390.21694.8
2.13-2.463.60.1553.43544397490.15595.6
2.46-3.023.50.1135.42938083760.11396.4
3.02-4.273.70.096.22376864690.0996.8
4.27-26.4873.80.0776.31365135570.07797.5

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation7 Å26.49 Å
Translation7 Å26.49 Å

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Processing

Software
NameVersionClassificationNB
SCALA3.3.16data scaling
PHASER2.5.2phasing
PHENIX1.8.1_1168refinement
PDB_EXTRACT3.11data extraction
BOSdata collection
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1WOM

1wom


Resolution: 1.35→26.487 Å / Occupancy max: 1 / Occupancy min: 0.21 / FOM work R set: 0.8494 / SU ML: 0.16 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 1.97 / Phase error: 23.16 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2161 4974 5.01 %random
Rwork0.1818 ---
obs0.1835 99269 85.84 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 67.07 Å2 / Biso mean: 20.2649 Å2 / Biso min: 4.48 Å2
Refinement stepCycle: LAST / Resolution: 1.35→26.487 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4148 0 22 640 4810
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064327
X-RAY DIFFRACTIONf_angle_d1.0555908
X-RAY DIFFRACTIONf_chiral_restr0.075674
X-RAY DIFFRACTIONf_plane_restr0.005771
X-RAY DIFFRACTIONf_dihedral_angle_d13.0131552
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.35-1.36540.3362950.31091767186249
1.3654-1.38140.31161030.32371807191049
1.3814-1.39830.3429940.30171998209254
1.3983-1.4160.31471110.29451858196952
1.416-1.43460.31291030.28962236233961
1.4346-1.45420.31171730.31223090326383
1.4542-1.4750.30991740.29843022319684
1.475-1.4970.28771370.2753026316382
1.497-1.52040.33111840.2623040322484
1.5204-1.54530.29521860.25263229341588
1.5453-1.5720.28891700.22073382355292
1.572-1.60060.24431730.20773358353192
1.6006-1.63140.28461730.20353398357192
1.6314-1.66460.23071890.19343347353693
1.6646-1.70080.24011520.19623409356193
1.7008-1.74040.24381940.19593408360293
1.7404-1.78390.22021800.18943418359893
1.7839-1.83210.24731710.18143441361294
1.8321-1.8860.22121920.18083430362294
1.886-1.94690.22641630.18943411357494
1.9469-2.01650.18281840.16683489367394
2.0165-2.09720.19281770.16883469364695
2.0972-2.19260.16791900.15413490368095
2.1926-2.30810.22041800.16643528370895
2.3081-2.45260.17481850.16233495368096
2.4526-2.64180.20181920.17013496368896
2.6418-2.90740.23411910.1793541373296
2.9074-3.32740.20811910.16513491368297
3.3274-4.18950.16291700.14593577374797
4.1895-26.49170.18411970.15183573377098

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