+Open data
-Basic information
Entry | Database: PDB / ID: 4dnp | ||||||
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Title | Crystal Structure of DAD2 | ||||||
Components | DAD2 | ||||||
Keywords | HYDROLASE / 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: 2.15 Å | ||||||
Authors | Hamiaux, C. | ||||||
Citation | 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 | 4dnp.cif.gz | 124.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4dnp.ent.gz | 98.1 KB | Display | PDB format |
PDBx/mmJSON format | 4dnp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dn/4dnp ftp://data.pdbj.org/pub/pdb/validation_reports/dn/4dnp | HTTPS FTP |
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-Related 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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Details | This protein behaves as a monomer on gel filtration column |
-Components
#1: Protein | Mass: 29861.180 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: gene was codon optimized for E.coli expression / 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*PLUS |
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#2: Chemical | ChemComp-DTV / ( |
#3: Chemical | ChemComp-GOL / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.01 Å3/Da / Density % sol: 59.18 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion / pH: 7.1 Details: (NH4)2HPO4 0.6M, pH 7.1, vapor diffusion, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.979417 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Mar 11, 2011 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.979417 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.15→40.876 Å / Num. all: 19684 / Num. obs: 19684 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 21.7 % / Biso Wilson estimate: 23.6 Å2 / Rmerge(I) obs: 0.126 / Rsym value: 0.126 / Net I/σ(I): 20.1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | Rfactor: 32.08 / Model details: Phaser MODE: MR_AUTO
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.15→40.876 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.928 / WRfactor Rfree: 0.2082 / WRfactor Rwork: 0.1658 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8912 / SU B: 8.332 / SU ML: 0.1 / SU R Cruickshank DPI: 0.1778 / SU Rfree: 0.1607 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.178 / ESU R Free: 0.161 / Stereochemistry target values: MAXIMUM LIKELIHOOD 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: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 71.69 Å2 / Biso mean: 26.5934 Å2 / Biso min: 8 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.15→40.876 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.15→2.206 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: -44.594 Å / Origin y: -43.472 Å / Origin z: 8.513 Å
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