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- PDB-5zhr: Crystal structure of OsD14 in complex with covalently bound KK094 -

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Basic information

Entry
Database: PDB / ID: 5zhr
TitleCrystal structure of OsD14 in complex with covalently bound KK094
ComponentsStrigolactone esterase D14
KeywordsHYDROLASE / Plant hormones / Plant signalling / Strigolactones / receptor
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
Chem-KOK / Strigolactone esterase D14
Similarity search - Component
Biological speciesOryza sativa subsp. japonica (Japanese rice)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsHirabayashi, K. / Miyakawa, T. / Tanokura, M.
Funding support Japan, 3items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)16H06736 Japan
Japan Society for the Promotion of Science (JSPS)17J04676 Japan
Japan Society for the Promotion of Science (JSPS)17K15258 Japan
CitationJournal: Mol Plant / Year: 2019
Title: Triazole Ureas Covalently Bind to Strigolactone Receptor and Antagonize Strigolactone Responses.
Authors: Nakamura, H. / Hirabayashi, K. / Miyakawa, T. / Kikuzato, K. / Hu, W. / Xu, Y. / Jiang, K. / Takahashi, I. / Niiyama, R. / Dohmae, N. / Tanokura, M. / Asami, T.
History
DepositionMar 13, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 21, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 23, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year
Revision 1.2Nov 22, 2023Group: 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
Revision 1.3Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)60,4774
Polymers60,0492
Non-polymers4282
Water9,476526
1
A: Strigolactone esterase D14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,2392
Polymers30,0241
Non-polymers2141
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Strigolactone esterase D14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,2392
Polymers30,0241
Non-polymers2141
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.250, 88.640, 119.380
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: 30024.361 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 (E. coli)
References: UniProt: Q10QA5, Hydrolases; Acting on ester bonds
#2: Chemical ChemComp-KOK / (2,3-dihydro-1H-indol-1-yl)(1H-1,2,3-triazol-1-yl)methanone


Mass: 214.223 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H10N4O / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 526 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.13 Å3/Da / Density % sol: 42.14 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: PEG 20000, MES

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1.1 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Jun 23, 2016
RadiationMonochromator: Cryo-cooled channel-cut Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.45→49.511 Å / Num. obs: 173170 / % possible obs: 99 % / Redundancy: 9.3 % / Rmerge(I) obs: 0.047 / Net I/σ(I): 26.3
Reflection shellResolution: 1.45→1.54 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.274 / Mean I/σ(I) obs: 5.9 / % possible all: 94

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3VXK

3vxk


Resolution: 1.45→49.511 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 18.22
RfactorNum. reflection% reflectionSelection details
Rfree0.1993 3809 2.2 %Random
Rwork0.1662 ---
obs0.1669 173170 98.74 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.45→49.511 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4102 0 22 526 4650
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0094218
X-RAY DIFFRACTIONf_angle_d1.2155748
X-RAY DIFFRACTIONf_dihedral_angle_d11.9961508
X-RAY DIFFRACTIONf_chiral_restr0.051662
X-RAY DIFFRACTIONf_plane_restr0.007744
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.45-1.46830.2751090.2285083X-RAY DIFFRACTION80
1.4683-1.48770.22211270.21575609X-RAY DIFFRACTION88
1.4877-1.5080.22871420.19656267X-RAY DIFFRACTION98
1.508-1.52960.2161390.19056324X-RAY DIFFRACTION100
1.5296-1.55240.18971420.18256402X-RAY DIFFRACTION100
1.5524-1.57670.23091430.17556250X-RAY DIFFRACTION100
1.5767-1.60250.21451460.16976414X-RAY DIFFRACTION100
1.6025-1.63020.16821460.16756314X-RAY DIFFRACTION100
1.6302-1.65980.2181410.17316385X-RAY DIFFRACTION100
1.6598-1.69170.21381430.16896304X-RAY DIFFRACTION100
1.6917-1.72630.21061430.16846387X-RAY DIFFRACTION100
1.7263-1.76380.22131440.17346305X-RAY DIFFRACTION100
1.7638-1.80480.20671490.17546414X-RAY DIFFRACTION100
1.8048-1.850.1951420.17136336X-RAY DIFFRACTION100
1.85-1.90.21871440.16876317X-RAY DIFFRACTION100
1.9-1.95590.19371470.16666386X-RAY DIFFRACTION100
1.9559-2.0190.20851400.16546370X-RAY DIFFRACTION100
2.019-2.09120.20621370.16596319X-RAY DIFFRACTION100
2.0912-2.17490.1871470.16366347X-RAY DIFFRACTION100
2.1749-2.27390.2231390.16686372X-RAY DIFFRACTION100
2.2739-2.39380.19661490.16366370X-RAY DIFFRACTION100
2.3938-2.54380.20061360.16736335X-RAY DIFFRACTION100
2.5438-2.74020.18961450.16696367X-RAY DIFFRACTION100
2.7402-3.01590.18271430.176349X-RAY DIFFRACTION100
3.0159-3.45220.18731430.16366354X-RAY DIFFRACTION100
3.4522-4.3490.20261420.14926353X-RAY DIFFRACTION100
4.349-49.53960.17831410.15476328X-RAY DIFFRACTION100

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