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- PDB-5yz7: Crystal structure of OsD14 in complex with D-ring-opened 7'-carba-4BD -

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Basic information

Entry
Database: PDB / ID: 5yz7
TitleCrystal structure of OsD14 in complex with D-ring-opened 7'-carba-4BD
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-94X / Strigolactone esterase D14
Similarity search - Component
Biological speciesOryza sativa Japonica Group (Japanese rice)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.898 Å
AuthorsHirabayashi, K. / Jiang, K. / Xu, Y. / Miyakawa, T. / Asami, 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: Plant Cell Physiol. / Year: 2018
Title: Rationally Designed Strigolactone Analogs as Antagonists of the D14 Receptor.
Authors: Takeuchi, J. / Jiang, K. / Hirabayashi, K. / Imamura, Y. / Wu, Y. / Xu, Y. / Miyakawa, T. / Nakamura, H. / Tanokura, M. / Asami, T.
History
DepositionDec 13, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 30, 2018Provider: repository / Type: Initial release
Revision 1.1Aug 29, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
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

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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)60,6194
Polymers60,0492
Non-polymers5702
Water7,837435
1
A: Strigolactone esterase D14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,3092
Polymers30,0241
Non-polymers2851
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Strigolactone esterase D14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,3092
Polymers30,0241
Non-polymers2851
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.501, 88.795, 118.600
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 Japonica Group (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-94X / (2Z,4S)-5-(4-bromophenyl)-4-hydroxy-2-methylpent-2-enoic acid


Mass: 285.134 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H13BrO3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 435 / 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: 2.13 Å3/Da / Density % sol: 42.16 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: PEG 20000, HEPES

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS VII / Detector: IMAGE PLATE / Date: Jan 20, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.898→50 Å / Num. obs: 76731 / % possible obs: 97.1 % / Redundancy: 13.9 % / Rmerge(I) obs: 0.054 / Net I/σ(I): 38.8
Reflection shellResolution: 1.9→2.01 Å / Redundancy: 13.2 % / Rmerge(I) obs: 0.238 / Mean I/σ(I) obs: 12.2 / % possible all: 89.4

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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: 1.898→37.543 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 22.62 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2273 3735 4.87 %Random
Rwork0.1892 ---
obs0.1911 76731 98.06 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.898→37.543 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4102 0 32 435 4569
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0054224
X-RAY DIFFRACTIONf_angle_d0.8625752
X-RAY DIFFRACTIONf_dihedral_angle_d12.8271504
X-RAY DIFFRACTIONf_chiral_restr0.033664
X-RAY DIFFRACTIONf_plane_restr0.003746
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8978-1.92180.4941190.47982339X-RAY DIFFRACTION84
1.9218-1.94710.48611280.40262334X-RAY DIFFRACTION85
1.9471-1.97380.27131390.21672755X-RAY DIFFRACTION100
1.9738-2.0020.2351410.19552741X-RAY DIFFRACTION100
2.002-2.03190.28241380.19362736X-RAY DIFFRACTION99
2.0319-2.06360.26371400.20142733X-RAY DIFFRACTION100
2.0636-2.09740.3041410.20822762X-RAY DIFFRACTION100
2.0974-2.13360.22051400.18072751X-RAY DIFFRACTION100
2.1336-2.17240.22361420.1832738X-RAY DIFFRACTION100
2.1724-2.21420.29131400.20492772X-RAY DIFFRACTION99
2.2142-2.25940.37441270.34362477X-RAY DIFFRACTION91
2.2594-2.30850.26491250.25082563X-RAY DIFFRACTION92
2.3085-2.36220.26651400.17862734X-RAY DIFFRACTION100
2.3622-2.42120.24171380.18542781X-RAY DIFFRACTION100
2.4212-2.48670.20121410.1792715X-RAY DIFFRACTION100
2.4867-2.55990.20821430.17522791X-RAY DIFFRACTION100
2.5599-2.64250.24711360.17872735X-RAY DIFFRACTION100
2.6425-2.73690.20641460.17682785X-RAY DIFFRACTION100
2.7369-2.84640.22271410.18282763X-RAY DIFFRACTION100
2.8464-2.97590.23181410.18812736X-RAY DIFFRACTION100
2.9759-3.13270.24051440.1792746X-RAY DIFFRACTION100
3.1327-3.32890.21311440.17312726X-RAY DIFFRACTION100
3.3289-3.58580.17851420.1642771X-RAY DIFFRACTION100
3.5858-3.94620.16731330.15722754X-RAY DIFFRACTION100
3.9462-4.51650.18031400.14252760X-RAY DIFFRACTION100
4.5165-5.68710.15891470.15552749X-RAY DIFFRACTION100
5.6871-37.55040.1831390.15032749X-RAY DIFFRACTION99

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