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- PDB-8vd3: Crystal Structure of D14 from Arabidopsis thaliana -

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Basic information

Entry
Database: PDB / ID: 8vd3
TitleCrystal Structure of D14 from Arabidopsis thaliana
ComponentsStrigolactone esterase D14
KeywordsHYDROLASE / Strigolactone / signalling / alpha/beta-hydrolase / phytohormone
Function / homology
Function and homology information


cellular response to strigolactone / 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
Similarity search - Domain/homology
Strigolactone esterase D14
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsGilio, A.K. / Shabek, N. / Guercio, A.M. / Pawlak, J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States) United States
CitationJournal: J.Biol.Chem. / Year: 2024
Title: Structural insights into rice KAI2 receptor provide functional implications for perception and signal transduction.
Authors: Guercio, A.M. / Gilio, A.K. / Pawlak, J. / Shabek, N.
History
DepositionDec 14, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 31, 2024Provider: repository / Type: Initial release
Revision 1.1Aug 7, 2024Group: Database references / Category: citation
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Aug 21, 2024Group: Database references / Category: citation / Item: _citation.journal_volume

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)59,3072
Polymers59,3072
Non-polymers00
Water4,179232
1
A: Strigolactone esterase D14


Theoretical massNumber of molelcules
Total (without water)29,6541
Polymers29,6541
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Strigolactone esterase D14


Theoretical massNumber of molelcules
Total (without water)29,6541
Polymers29,6541
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)43.692, 69.267, 90.800
Angle α, β, γ (deg.)90.00, 93.38, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Strigolactone esterase D14 / Protein DWARF 14 / AtD14


Mass: 29653.727 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: D14, At3g03990, T11I18.10 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9SQR3, Hydrolases; Acting on ester bonds
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 232 / 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: 2.34 Å3/Da / Density % sol: 47.45 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 0.15M Ammonium acetate, 0.01M Calcium chloride dihydrate, 0.1M Tris pH 8.5, 28% broad PEG smear from BCS (Molecular Dimensions)

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Data collection

DiffractionMean temperature: 298 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Dec 12, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→45.32 Å / Num. obs: 36532 / % possible obs: 99.3 % / Redundancy: 5.8 % / Rsym value: 0.043 / Net I/σ(I): 14.6
Reflection shellResolution: 2→2.05 Å / Num. unique obs: 2459 / Rsym value: 0.317

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→45.32 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.947 / SU B: 4.621 / SU ML: 0.123 / Cross valid method: THROUGHOUT / ESU R: 0.167 / ESU R Free: 0.15 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20724 1915 5.2 %RANDOM
Rwork0.16255 ---
obs0.16495 34600 99.28 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.665 Å2
Baniso -1Baniso -2Baniso -3
1--1.41 Å2-0 Å2-2.35 Å2
2--1.54 Å20 Å2
3---0.15 Å2
Refinement stepCycle: 1 / Resolution: 2→45.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4125 0 0 232 4357
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0124224
X-RAY DIFFRACTIONr_bond_other_d0.0010.0163968
X-RAY DIFFRACTIONr_angle_refined_deg1.5591.8095757
X-RAY DIFFRACTIONr_angle_other_deg0.5431.7289074
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2925526
X-RAY DIFFRACTIONr_dihedral_angle_2_deg10.479534
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.96610645
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0760.2656
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.025064
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021036
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.5253.0722110
X-RAY DIFFRACTIONr_mcbond_other2.5243.0712110
X-RAY DIFFRACTIONr_mcangle_it3.5745.5092634
X-RAY DIFFRACTIONr_mcangle_other3.5735.512635
X-RAY DIFFRACTIONr_scbond_it3.6523.5692114
X-RAY DIFFRACTIONr_scbond_other3.6513.572115
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.7476.3423124
X-RAY DIFFRACTIONr_long_range_B_refined7.11534.014802
X-RAY DIFFRACTIONr_long_range_B_other7.10733.654751
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.05 Å
RfactorNum. reflection% reflection
Rfree0.291 110 -
Rwork0.265 2343 -
obs--91.63 %

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