+Open data
-Basic information
Entry | Database: PDB / ID: 6uh9 | ||||||
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Title | Crystal structure of DAD2 D166A mutant | ||||||
Components | Decreased Apical Dominance 2 | ||||||
Keywords | HYDROLASE / Strigolactone receptor / DAD2 | ||||||
Function / homology | Function and homology information strigolactone biosynthetic process / secondary shoot formation / hydrolase activity, acting on ester bonds / Hydrolases; Acting on ester bonds / hydrolase activity Similarity search - Function | ||||||
Biological species | Petunia hybrida (garden petunia) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.52 Å | ||||||
Authors | Sharma, P. / Hamiaux, C. / Snowden, K.C. | ||||||
Funding support | New Zealand, 1items
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Citation | Journal: J.Biol.Chem. / Year: 2020 Title: Flexibility of the petunia strigolactone receptor DAD2 promotes its interaction with signaling partners. Authors: Lee, H.W. / Sharma, P. / Janssen, B.J. / Drummond, R.S.M. / Luo, Z. / Hamiaux, C. / Collier, T. / Allison, J.R. / Newcomb, R.D. / Snowden, K.C. #1: Journal: Curr. Biol. / Year: 2012 Title: DAD2 is an alpha/beta hydrolase likely to be involved in the perception of the plant branching hormone, strigolactone. Authors: Hamiaux, C. / Drummond, R.S. / Janssen, B.J. / Ledger, S.E. / Cooney, J.M. / Newcomb, R.D. / Snowden, K.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6uh9.cif.gz | 234.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6uh9.ent.gz | 185.3 KB | Display | PDB format |
PDBx/mmJSON format | 6uh9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6uh9_validation.pdf.gz | 444.6 KB | Display | wwPDB validaton report |
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Full document | 6uh9_full_validation.pdf.gz | 449.6 KB | Display | |
Data in XML | 6uh9_validation.xml.gz | 28.2 KB | Display | |
Data in CIF | 6uh9_validation.cif.gz | 44 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uh/6uh9 ftp://data.pdbj.org/pub/pdb/validation_reports/uh/6uh9 | HTTPS FTP |
-Related structure data
Related structure data | 6uh8C 4dnpS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: GLN / Beg label comp-ID: GLN / End auth comp-ID: HIS / End label comp-ID: HIS / Refine code: _ / Auth seq-ID: 3 - 266 / Label seq-ID: 5 - 268
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-Components
#1: Protein | Mass: 29842.152 Da / Num. of mol.: 2 / Mutation: D166A, C89Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) Petunia hybrida (garden petunia) / Gene: dad2 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta Gami 2 / References: UniProt: L7MTK5, UniProt: J9U5U9*PLUS #2: Chemical | ChemComp-PG4 / | #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.08 Å3/Da / Density % sol: 40.48 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 0.1 M Trizma-acetate-bicine (pH 8.5), 0.06 M divalents (MgCl2 and CaCl2), 45-55% PEG 500 MME PEG 20000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å | ||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Jun 20, 2018 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.52→30.33 Å / Num. obs: 75017 / % possible obs: 95.1 % / Redundancy: 3.9 % / CC1/2: 0.997 / Rmerge(I) obs: 0.089 / Rpim(I) all: 0.052 / Rrim(I) all: 0.104 / Net I/σ(I): 7.8 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | Model details: Phaser MODE: MR_AUTO
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4DNP Resolution: 1.52→30.33 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.95 / SU B: 3.722 / SU ML: 0.068 / SU R Cruickshank DPI: 0.0832 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.083 / ESU R Free: 0.082 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 134.22 Å2 / Biso mean: 17.78 Å2 / Biso min: 8.27 Å2
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Refinement step | Cycle: final / Resolution: 1.52→30.33 Å
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Refine LS restraints |
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Refine LS restraints NCS | Ens-ID: 1 / Number: 8564 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.09 Å / Weight position: 0.05
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LS refinement shell | Resolution: 1.52→1.559 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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