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- PDB-8z53: Arabidopsis Dwarf14 (AtD14) co-crystallized in the presence of Za... -

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Basic information

Entry
Database: PDB / ID: 8z53
TitleArabidopsis Dwarf14 (AtD14) co-crystallized in the presence of Zaxinone
ComponentsStrigolactone esterase D14
KeywordsHYDROLASE / AtD14 / Zaxinone / Strigolactone
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
: / DI(HYDROXYETHYL)ETHER / Strigolactone esterase D14
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsArold, S.T. / Hameed, U.F.S.
Funding support Saudi Arabia, 1items
OrganizationGrant numberCountry
Other privateKing Abdullah University of Science and Technology Saudi Arabia
CitationJournal: To Be Published
Title: Arabidopsis Dwarf14 (AtD14) co-crystallized in the presence of Zaxinone
Authors: Arold, S.T. / Hameed, U.F.S.
History
DepositionApr 18, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 23, 2025Provider: repository / Type: Initial release
Revision 2.0Jun 11, 2025Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Data collection / Database references / Derived calculations / Other / Polymer sequence / Refinement description / Source and taxonomy / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / atom_sites / cell / entity / entity_name_com / entity_poly / entity_poly_seq / entity_src_gen / pdbx_contact_author / pdbx_distant_solvent_atoms / pdbx_entity_instance_feature / pdbx_entity_nonpoly / pdbx_entry_details / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_refine_tls / pdbx_refine_tls_group / pdbx_struct_assembly / pdbx_struct_assembly_auth_evidence / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_residues / pdbx_validate_close_contact / pdbx_validate_planes / pdbx_validate_torsion / refine / refine_hist / refine_ls_restr / refine_ls_shell / reflns_shell / software / struct_asym / struct_conf / struct_ref / struct_ref_seq / struct_sheet / struct_sheet_order / struct_sheet_range
Item: _atom_sites.fract_transf_matrix[2][1] / _atom_sites.fract_transf_matrix[3][2] ..._atom_sites.fract_transf_matrix[2][1] / _atom_sites.fract_transf_matrix[3][2] / _cell.Z_PDB / _pdbx_distant_solvent_atoms.auth_seq_id / _pdbx_distant_solvent_atoms.neighbor_ligand_distance / _pdbx_distant_solvent_atoms.neighbor_macromolecule_distance / _pdbx_entity_nonpoly.entity_id / _pdbx_entry_details.nonpolymer_details / _pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details / _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details / _refine.B_iso_mean / _refine.aniso_B[1][1] / _refine.aniso_B[1][2] / _refine.aniso_B[1][3] / _refine.aniso_B[2][2] / _refine.aniso_B[2][3] / _refine.aniso_B[3][3] / _refine.correlation_coeff_Fo_to_Fc / _refine.correlation_coeff_Fo_to_Fc_free / _refine.details / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_R_factor_obs / _refine.overall_SU_B / _refine.overall_SU_ML / _refine.pdbx_overall_ESU_R / _refine.pdbx_overall_ESU_R_Free / _refine.pdbx_solvent_ion_probe_radii / _refine.pdbx_solvent_shrinkage_radii / _refine.pdbx_solvent_vdw_probe_radii / _refine.pdbx_stereochemistry_target_values / _refine.solvent_model_details / _refine_hist.number_atoms_solvent / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_protein / _refine_ls_shell.R_factor_R_free / _refine_ls_shell.R_factor_R_work / _refine_ls_shell.d_res_low / _refine_ls_shell.number_reflns_R_free / _refine_ls_shell.number_reflns_R_work / _refine_ls_shell.pdbx_total_number_of_bins_used / _refine_ls_shell.percent_reflns_obs / _reflns_shell.meanI_over_sigI_obs / _reflns_shell.pdbx_redundancy / _reflns_shell.percent_possible_all / _software.version / _struct_conf.beg_auth_asym_id / _struct_conf.beg_auth_comp_id / _struct_conf.beg_auth_seq_id / _struct_conf.beg_label_asym_id / _struct_conf.beg_label_comp_id / _struct_conf.beg_label_seq_id / _struct_conf.end_auth_asym_id / _struct_conf.end_auth_comp_id / _struct_conf.end_auth_seq_id / _struct_conf.end_label_asym_id / _struct_conf.end_label_comp_id / _struct_conf.end_label_seq_id / _struct_conf.pdbx_PDB_helix_class / _struct_conf.pdbx_PDB_helix_length / _struct_sheet_range.beg_auth_asym_id / _struct_sheet_range.beg_auth_comp_id / _struct_sheet_range.beg_auth_seq_id / _struct_sheet_range.beg_label_asym_id / _struct_sheet_range.beg_label_comp_id / _struct_sheet_range.beg_label_seq_id / _struct_sheet_range.end_auth_asym_id / _struct_sheet_range.end_auth_comp_id / _struct_sheet_range.end_auth_seq_id / _struct_sheet_range.end_label_asym_id / _struct_sheet_range.end_label_comp_id / _struct_sheet_range.end_label_seq_id / _struct_sheet_range.id / _struct_sheet_range.sheet_id
Description: Ligand geometry / Provider: author / Type: Coordinate replacement

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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)59,4786
Polymers58,7312
Non-polymers7474
Water1,11762
1
A: Strigolactone esterase D14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,8384
Polymers29,3651
Non-polymers4733
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Strigolactone esterase D14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,6402
Polymers29,3651
Non-polymers2741
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)43.820, 69.580, 89.860
Angle α, β, γ (deg.)90.00, 92.85, 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: 29365.334 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 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q9SQR3, Hydrolases; Acting on ester bonds
#2: Chemical ChemComp-A1L1M / (7E)-6-methyl-8-[(4S)-2,6,6-trimethyl-4-oxidanyl-cyclohexen-1-yl]octa-3,5,7-trien-2-one


Mass: 274.398 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H26O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 62 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN
Nonpolymer detailsThe authors state that the ligand in this structure is indeed Zaxinone: (3E,5E,7E)-6-Methyl-8-[(4R)- ...The authors state that the ligand in this structure is indeed Zaxinone: (3E,5E,7E)-6-Methyl-8-[(4R)-2,6,6-trimethyl-4-hydroxy-1-cyclohexenyl]-3,5,7-octatriene-2-one, and stereoisomer was changed as the hydroxyl group directly forms a strong hydrogen bonding with Ser 97.

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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: 47.5 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Potassium sodium tartrate tetrahydrate, 20% w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.988 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 26, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.988 Å / Relative weight: 1
ReflectionResolution: 2.4→44.91 Å / Num. obs: 20924 / % possible obs: 98.49 % / Redundancy: 6.6 % / CC1/2: 0.999 / Net I/σ(I): 17.77
Reflection shellResolution: 2.4→2.48 Å / Redundancy: 4.6 % / Mean I/σ(I) obs: 2.77 / Num. unique obs: 1788 / CC1/2: 0.85 / % possible all: 90

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Processing

Software
NameVersionClassification
REFMACrefmac5refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→44.91 Å / SU B: 17.216 / SU ML: 0.187 / Cross valid method: THROUGHOUT / ESU R: 0.525 / ESU R Free: 0.257 / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.2264 1047 5 %RANDOM
Rwork0.17772 ---
obs0.18016 19877 98.49 %-
Displacement parametersBiso mean: 38.844 Å2
Baniso -1Baniso -2Baniso -3
1--0.86 Å20 Å2-0.36 Å2
2--0.48 Å20 Å2
3---0.41 Å2
Refinement stepCycle: LAST / Resolution: 2.4→44.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4123 0 53 62 4238
LS refinement shellResolution: 2.4→2.48 Å
RfactorNum. reflection% reflection
Rfree0.3169 --
Rwork0.2917 8268 -
obs--90 %

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