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- PDB-4jyp: crystal Structure of KAI2 Apo form -

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Basic information

Entry
Database: PDB / ID: 4jyp
Titlecrystal Structure of KAI2 Apo form
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
Probable esterase KAI2
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / molecular replacement / Resolution: 1.3 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 31, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 8, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2013Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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


Theoretical massNumber of molelcules
Total (without water)59,6322
Polymers59,6322
Non-polymers00
Water13,709761
1
A: Hydrolase, alpha/beta fold family protein


Theoretical massNumber of molelcules
Total (without water)29,8161
Polymers29,8161
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Hydrolase, alpha/beta fold family protein


Theoretical massNumber of molelcules
Total (without water)29,8161
Polymers29,8161
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)50.690, 53.210, 55.770
Angle α, β, γ (deg.)89.49, 89.76, 63.84
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: AT4g37470, F6G17.120, KAI2 / Plasmid: pET28 / 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.: 761 / 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: 2.26 Å3/Da / Density % sol: 45.67 %
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: 1.3→26.488 Å / Num. all: 115956 / Num. obs: 115956 / % possible obs: 90.1 % / Redundancy: 2.3 % / Rpim(I) all: 0.064 / Rrim(I) all: 0.109 / Rsym value: 0.088 / Net I/av σ(I): 3.794 / Net I/σ(I): 6.7 / Num. measured all: 261965

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.5 Å27.88 Å
Translation2.5 Å27.88 Å

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.3.16data scaling
PHASER2.4.0phasing
PHENIX1.8.1_1168refinement
PDB_EXTRACT3.11data extraction
BOSdata collection
RefinementResolution: 1.3→26.488 Å / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.8883 / SU ML: 0.13 / σ(F): 1.97 / Phase error: 19.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1906 5837 5.04 %
Rwork0.1688 110071 -
obs0.1699 115908 90.11 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 56.82 Å2 / Biso mean: 14.1245 Å2 / Biso min: 2.11 Å2
Refinement stepCycle: LAST / Resolution: 1.3→26.488 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4148 0 0 761 4909
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064343
X-RAY DIFFRACTIONf_angle_d1.0915938
X-RAY DIFFRACTIONf_dihedral_angle_d12.2741586
X-RAY DIFFRACTIONf_chiral_restr0.074683
X-RAY DIFFRACTIONf_plane_restr0.005776
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3-1.31480.37411240.3112621X-RAY DIFFRACTION66
1.3148-1.33020.28411510.28322886X-RAY DIFFRACTION70
1.3302-1.34650.29151580.26452828X-RAY DIFFRACTION70
1.3465-1.36350.26081770.24462833X-RAY DIFFRACTION70
1.3635-1.38150.32011500.22952874X-RAY DIFFRACTION71
1.3815-1.40040.22342010.22893778X-RAY DIFFRACTION91
1.4004-1.42040.22271980.21573676X-RAY DIFFRACTION92
1.4204-1.44160.23031870.20293804X-RAY DIFFRACTION92
1.4416-1.46410.19692260.19993659X-RAY DIFFRACTION92
1.4641-1.48810.21941720.19553803X-RAY DIFFRACTION92
1.4881-1.51380.21642080.18213753X-RAY DIFFRACTION93
1.5138-1.54130.18682150.17353771X-RAY DIFFRACTION92
1.5413-1.57090.16771710.16073837X-RAY DIFFRACTION93
1.5709-1.6030.18352330.15613743X-RAY DIFFRACTION93
1.603-1.63780.17051920.16413817X-RAY DIFFRACTION93
1.6378-1.67590.2021930.16263818X-RAY DIFFRACTION94
1.6759-1.71780.19832080.16293832X-RAY DIFFRACTION94
1.7178-1.76430.17771870.16293839X-RAY DIFFRACTION94
1.7643-1.81620.19472110.16543847X-RAY DIFFRACTION95
1.8162-1.87480.1771880.15873895X-RAY DIFFRACTION95
1.8748-1.94180.21262010.16333843X-RAY DIFFRACTION95
1.9418-2.01950.18442070.15843894X-RAY DIFFRACTION95
2.0195-2.11140.18692010.15473881X-RAY DIFFRACTION95
2.1114-2.22260.17092110.15143922X-RAY DIFFRACTION96
2.2226-2.36180.15482050.1543871X-RAY DIFFRACTION96
2.3618-2.5440.17672110.15853927X-RAY DIFFRACTION96
2.544-2.79980.17882040.17223938X-RAY DIFFRACTION97
2.7998-3.20430.19532040.16423914X-RAY DIFFRACTION97
3.2043-4.03480.17842180.14673971X-RAY DIFFRACTION98
4.0348-26.49380.18172250.16833996X-RAY DIFFRACTION98

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