+
Open data
-
Basic information
Entry | Database: PDB / ID: 6ap6 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal Structure of DAD2 in complex with tolfenamic acid | |||||||||
![]() | Probable strigolactone esterase DAD2 | |||||||||
![]() | PLANT PROTEIN / alpha/beta hydrolase | |||||||||
Function / homology | ![]() strigolactone biosynthetic process / secondary shoot formation / hydrolase activity, acting on ester bonds / Hydrolases; Acting on ester bonds Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() ![]() | |||||||||
![]() | Hamiaux, C. | |||||||||
Funding support | ![]()
| |||||||||
![]() | ![]() 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 |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 232.3 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 184.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1004 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 1006.6 KB | Display | |
Data in XML | ![]() | 25.6 KB | Display | |
Data in CIF | ![]() | 37.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6ap7C ![]() 6ap8C ![]() 4dnpS S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||||||||||||
2 | ![]()
| ||||||||||||||||||
Unit cell |
| ||||||||||||||||||
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
|
-
Components
#1: Protein | Mass: 29886.164 Da / Num. of mol.: 2 / Mutation: C89Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.27 Å3/Da / Density % sol: 45.71 % / Description: Rod |
---|---|
Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: Tris/Acetate 0.1M, MgCl2 0.2M, PEG 8000 24% |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Feb 24, 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: 1.65→34.67 Å / Num. obs: 56704 / % possible obs: 91.2 % / Redundancy: 3.9 % / Biso Wilson estimate: 16.3 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.086 / Rpim(I) all: 0.051 / Rrim(I) all: 0.1 / Net I/σ(I): 10.9 | ||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
|
-Phasing
Phasing | Method: ![]() | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Phasing MR | Model details: Phaser MODE: MR_AUTO
|
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 4DNP Resolution: 1.65→30.42 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.949 / SU B: 4.764 / SU ML: 0.08 / SU R Cruickshank DPI: 0.1072 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.107 / ESU R Free: 0.103 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.3 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 161.08 Å2 / Biso mean: 21.885 Å2 / Biso min: 7.01 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.65→30.42 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints NCS | Ens-ID: 1 / Number: 32966 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.08 Å / Weight position: 0.05
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.65→1.693 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|