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Yorodumi- PDB-5z8p: Structural basis for specific inhibition of highly sensitive ShHT... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5z8p | ||||||
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Title | Structural basis for specific inhibition of highly sensitive ShHTL7 receptor | ||||||
Components | Hyposensitive to light 7 | ||||||
Keywords | HYDROLASE / Strigolactone receptor / Striga germination signaling | ||||||
Function / homology | Alpha/beta hydrolase family / Alpha/beta hydrolase fold-1 / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / Hyposensitive to light 7 Function and homology information | ||||||
Biological species | Striga hermonthica (purple witchweed) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å | ||||||
Authors | Hameed, U.S. / Arold, S.T. | ||||||
Funding support | Saudi Arabia, 1items
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Citation | Journal: EMBO Rep. / Year: 2018 Title: Structural basis for specific inhibition of the highly sensitive ShHTL7 receptor. Authors: Shahul Hameed, U. / Haider, I. / Jamil, M. / Kountche, B.A. / Guo, X. / Zarban, R.A. / Kim, D. / Al-Babili, S. / Arold, S.T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5z8p.cif.gz | 132.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5z8p.ent.gz | 102.1 KB | Display | PDB format |
PDBx/mmJSON format | 5z8p.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z8/5z8p ftp://data.pdbj.org/pub/pdb/validation_reports/z8/5z8p | HTTPS FTP |
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-Related structure data
Related structure data | 5z82C 5z89C 5z95C 5cbkS C: citing same article (ref.) 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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Unit cell |
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-Components
#1: Protein | Mass: 30610.168 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Striga hermonthica (purple witchweed) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0M3PNA2 |
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#2: 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: 3.19 Å3/Da / Density % sol: 61.41 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.1 M MES monohydrate pH 6.5, 1.6 M Magnesium sulfate heptahydrate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.987 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jan 21, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.987 Å / Relative weight: 1 |
Reflection | Resolution: 1.35→40.09 Å / Num. obs: 85478 / % possible obs: 99.61 % / Redundancy: 9.1 % / CC1/2: 0.999 / Net I/σ(I): 23.12 |
Reflection shell | Resolution: 1.35→1.398 Å / CC1/2: 0.575 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5CBK Resolution: 1.35→40.09 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.979 / SU B: 1.415 / SU ML: 0.024 / Cross valid method: THROUGHOUT / ESU R: 0.036 / ESU R Free: 0.035 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.1 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.335 Å2
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Refinement step | Cycle: 1 / Resolution: 1.35→40.09 Å
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Refine LS restraints |
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