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- PDB-6ap8: Crystal Structure of rice D14 bound to 2-(2-methyl-3-nitroanilino... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6ap8 | |||||||||
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Title | Crystal Structure of rice D14 bound to 2-(2-methyl-3-nitroanilino)benzoic acid | |||||||||
![]() | Strigolactone esterase D14 | |||||||||
![]() | PLANT PROTEIN / alpha/beta hydrolase | |||||||||
Function / homology | ![]() strigolactone biosynthetic process / secondary shoot formation / Hydrolases; Acting on ester bonds / hydrolase activity / nucleus / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() ![]() | |||||||||
![]() | Hamiaux, C. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Inhibition of strigolactone receptors byN-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. #1: ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 253.8 KB | Display | ![]() |
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PDB format | ![]() | 203.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 998.3 KB | Display | ![]() |
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Full document | ![]() | 1007.9 KB | Display | |
Data in XML | ![]() | 29 KB | Display | |
Data in CIF | ![]() | 44.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6ap6C ![]() 6ap7C ![]() 3w04S S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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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: GLY / Beg label comp-ID: GLY / End auth comp-ID: ARG / End label comp-ID: ARG / Refine code: _ / Auth seq-ID: 53 - 317 / Label seq-ID: 4 - 268
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Details | Monomer as determined by gel filtration |
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Components
#1: Protein | Mass: 29366.695 Da / Num. of mol.: 2 / Fragment: residues 52-318 Source method: isolated from a genetically manipulated source Details: gene was codon optimized for E.coli expression Source: (gene. exp.) ![]() ![]() Gene: D14, D88, HTD2, Os03g0203200, LOC_Os03g10620 / Plasmid: pDEST566 / Production host: ![]() ![]() References: UniProt: Q10QA5, Hydrolases; Acting on ester bonds #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.16 Å3/Da / Density % sol: 43.03 % / Description: Rod |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: HEPES 0.1M, MPD 5%, PEG 6000 8% |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Nov 20, 2015 | ||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 | ||||||||||||||||||||||||
Reflection | Resolution: 1.27→48.01 Å / Num. obs: 134179 / % possible obs: 100 % / Redundancy: 14.5 % / Biso Wilson estimate: 10.3 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.154 / Rpim(I) all: 0.042 / Rrim(I) all: 0.159 / Net I/σ(I): 12 | ||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: ![]() | |||||||||
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Phasing MR | Model details: Phaser MODE: MR_AUTO
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3W04 Resolution: 1.27→44.52 Å / Cor.coef. Fo:Fc: 0.983 / Cor.coef. Fo:Fc free: 0.972 / SU B: 1.573 / SU ML: 0.029 / SU R Cruickshank DPI: 0.0382 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.038 / ESU R Free: 0.04 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.2 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 77.57 Å2 / Biso mean: 13.154 Å2 / Biso min: 4.49 Å2
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Refinement step | Cycle: final / Resolution: 1.27→44.52 Å
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Refine LS restraints |
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Refine LS restraints NCS | Ens-ID: 1 / Number: 31812 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.13 Å / Weight position: 0.05
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LS refinement shell | Resolution: 1.27→1.303 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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