+Open data
-Basic information
Entry | Database: PDB / ID: 6o5j | ||||||
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Title | Crystal Structure of DAD2 bound to quinazolinone derivative | ||||||
Components | Probable strigolactone esterase DAD2 | ||||||
Keywords | HORMONE / alpha/beta hydrolase | ||||||
Function / homology | Function and homology information strigolactone biosynthetic process / secondary shoot formation / hydrolase activity, acting on ester bonds / Hydrolases; Acting on ester bonds Similarity search - Function | ||||||
Biological species | Petunia hybrida (garden petunia) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.63 Å | ||||||
Authors | Hamiaux, C. | ||||||
Funding support | New Zealand, 1items
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Citation | Journal: Biochem.J. / Year: 2019 Title: Chemical synthesis and characterization of a new quinazolinedione competitive antagonist for strigolactone receptors with an unexpected binding mode. Authors: Hamiaux, C. / Larsen, L. / Lee, H.W. / Luo, Z. / Sharma, P. / Hawkins, B.C. / Perry, N.B. / Snowden, K.C. #1: Journal: J. Biol. Chem. / Year: 2018 Title: Inhibition of strigolactone receptors by N-phenylanthranilic acid derivatives: Structural and functional insights Authors: Hamiaux, C. / Drummond, R.S.M. / Luo, Z. / Lee, H.W. / Sharma, P. / Janssen, B.J. / Perry, N.B. / Denny, W.A. / Snowden, K.C. #2: Journal: Curr. Biol. / Year: 2012 Title: DAD2 is an a/b 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 | 6o5j.cif.gz | 237.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6o5j.ent.gz | 189.7 KB | Display | PDB format |
PDBx/mmJSON format | 6o5j.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6o5j_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 6o5j_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 6o5j_validation.xml.gz | 27.8 KB | Display | |
Data in CIF | 6o5j_validation.cif.gz | 40.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o5/6o5j ftp://data.pdbj.org/pub/pdb/validation_reports/o5/6o5j | HTTPS FTP |
-Related structure data
Related structure data | 4dnpS S: Starting model for refinement |
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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: 1 - 264
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 29426.623 Da / Num. of mol.: 2 / Mutation: C89Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) Petunia hybrida (garden petunia) / Gene: DAD2 / Plasmid: pDEST566 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta gami 2 References: UniProt: J9U5U9, Hydrolases; Acting on ester bonds |
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-Non-polymers , 5 types, 520 molecules
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-ACT / | #5: Chemical | ChemComp-PEG / | #6: Water | ChemComp-HOH / | |
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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: 2.28 Å3/Da / Density % sol: 45.98 % / Mosaicity: 0.64 ° |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion / pH: 8.5 / Details: 0.1M Tris/Acetate, 0.2M MgCl2, 31% PEG 3350 |
-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: Feb 25, 2016 | ||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 | ||||||||||||||||||||||||
Reflection | Resolution: 1.63→31.3 Å / Num. obs: 62194 / % possible obs: 96 % / Redundancy: 3.9 % / CC1/2: 0.998 / Rmerge(I) obs: 0.08 / Rpim(I) all: 0.047 / Rrim(I) all: 0.092 / Net I/σ(I): 11.8 | ||||||||||||||||||||||||
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: 1.63→29.37 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.955 / SU B: 3.659 / SU ML: 0.063 / SU R Cruickshank DPI: 0.0889 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.089 / ESU R Free: 0.091 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
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Solvent computation | Ion probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 194.67 Å2 / Biso mean: 18.483 Å2 / Biso min: 5.84 Å2
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Refinement step | Cycle: final / Resolution: 1.63→29.37 Å
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Refine LS restraints |
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Refine LS restraints NCS | Ens-ID: 1 / Number: 8761 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.08 Å / Weight position: 0.05
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LS refinement shell | Resolution: 1.63→1.672 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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Refinement TLS params. | T11: 0.0087 Å2 / Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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