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- PDB-6elx: Oryza sativa DWARF14 -

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Basic information

Entry
Database: PDB / ID: 6elx
TitleOryza sativa DWARF14
ComponentsStrigolactone esterase D14
KeywordsHYDROLASE / Strigolactone / strigolactone receptor / D14 / ligand binding
Function / homology
Function and homology information


strigolactone biosynthetic process / secondary shoot formation / Hydrolases; Acting on ester bonds / hydrolase activity / nucleus / cytoplasm
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
Strigolactone esterase D14
Similarity search - Component
Biological speciesOryza sativa subsp. japonica (Japanese rice)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å
AuthorsAndersson, I. / Carlsson, G.H. / Hasse, D.
CitationJournal: J. Exp. Bot. / Year: 2018
Title: The elusive ligand complexes of the DWARF14 strigolactone receptor.
Authors: Carlsson, G.H. / Hasse, D. / Cardinale, F. / Prandi, C. / Andersson, I.
History
DepositionSep 29, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 9, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: 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

Downloads & links

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Assembly

Deposited unit
A: Strigolactone esterase D14
B: Strigolactone esterase D14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,38611
Polymers58,5052
Non-polymers8819
Water10,899605
1
A: Strigolactone esterase D14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,6475
Polymers29,2531
Non-polymers3944
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Strigolactone esterase D14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,7396
Polymers29,2531
Non-polymers4875
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.120, 88.640, 118.940
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 Strigolactone esterase D14 / Protein DWARF 14 / Protein DWARF 88 / Protein HIGH-TILLERING DWARF 2


Mass: 29252.594 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryza sativa subsp. japonica (Japanese rice)
Gene: D14, D88, HTD2, Os03g0203200, LOC_Os03g10620 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q10QA5, Hydrolases; Acting on ester bonds
#2: Chemical ChemComp-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 605 / 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: 2.17 Å3/Da / Density % sol: 42 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: HEPES pH 7.0, 2-methylpentandiol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.99188 Å
DetectorType: DECTRIS PILATUS3 X 2M / Detector: PIXEL / Date: Nov 21, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99188 Å / Relative weight: 1
ReflectionResolution: 1.35→44.61 Å / Num. obs: 107538 / % possible obs: 95.7 % / Redundancy: 4.8 % / Biso Wilson estimate: 12.45 Å2 / Rmerge(I) obs: 0.05099 / Net I/σ(I): 16.15
Reflection shellResolution: 1.35→1.4 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.4184 / % possible all: 77.3

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Processing

Software
NameVersionClassification
PHENIX(DEV_2880: ???)refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1WOM

1wom


Resolution: 1.35→44.61 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / Phase error: 17.33
RfactorNum. reflection% reflectionSelection details
Rfree0.177 5357 5.02 %Random selection
Rwork0.159 ---
obs0.161 107538 95.7 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.35→44.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4122 0 58 605 4785
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0054579
X-RAY DIFFRACTIONf_angle_d0.7856298
X-RAY DIFFRACTIONf_dihedral_angle_d2.9183331
X-RAY DIFFRACTIONf_chiral_restr0.076729
X-RAY DIFFRACTIONf_plane_restr0.005823
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3-1.31480.23771290.23392069X-RAY DIFFRACTION54
1.3148-1.33020.25531440.22862291X-RAY DIFFRACTION58
1.3302-1.34650.23791260.21632482X-RAY DIFFRACTION63
1.3465-1.36350.2231300.21082737X-RAY DIFFRACTION69
1.3635-1.38150.23491370.21383019X-RAY DIFFRACTION76
1.3815-1.40040.21861790.21623343X-RAY DIFFRACTION86
1.4004-1.42040.22311870.20023764X-RAY DIFFRACTION94
1.4204-1.44160.23752000.19753788X-RAY DIFFRACTION97
1.4416-1.46410.23462030.18983782X-RAY DIFFRACTION96
1.4641-1.48810.21362040.18973800X-RAY DIFFRACTION97
1.4881-1.51380.20452110.17653839X-RAY DIFFRACTION97
1.5138-1.54130.18492000.17613795X-RAY DIFFRACTION97
1.5413-1.5710.192060.17553835X-RAY DIFFRACTION97
1.571-1.6030.1861910.16853775X-RAY DIFFRACTION95
1.603-1.63790.20152080.16363867X-RAY DIFFRACTION98
1.6379-1.6760.17042110.16263876X-RAY DIFFRACTION98
1.676-1.71790.19891980.16273855X-RAY DIFFRACTION97
1.7179-1.76440.18412080.16143890X-RAY DIFFRACTION99
1.7644-1.81630.19042070.15833884X-RAY DIFFRACTION98
1.8163-1.87490.17082000.17023853X-RAY DIFFRACTION97
1.8749-1.94190.16912110.16073917X-RAY DIFFRACTION98
1.9419-2.01970.17782060.15473936X-RAY DIFFRACTION99
2.0197-2.11160.16682080.14863947X-RAY DIFFRACTION99
2.1116-2.22290.17232040.14683932X-RAY DIFFRACTION99
2.2229-2.36220.16532100.15073971X-RAY DIFFRACTION99
2.3622-2.54450.1742120.1543957X-RAY DIFFRACTION99
2.5445-2.80060.18392070.15774028X-RAY DIFFRACTION100
2.8006-3.20570.15742140.15524046X-RAY DIFFRACTION99
3.2057-4.03840.1762150.1384042X-RAY DIFFRACTION99
4.0384-44.63390.15272210.15514243X-RAY DIFFRACTION99

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