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Open data
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Basic information
Entry | Database: PDB / ID: 5mg9 | ||||||
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Title | Putative Ancestral Mamba toxin 1 (AncTx1-W28R/I38S) | ||||||
![]() | AncTx1-W28R/I38S | ||||||
![]() | TOXIN / Ancestral mamba snake toxin / three-finger fold / Ancestral toxin resurrection and engineering / aminergic toxin | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Stura, E.A. / Tepshi, L. / Blanchet, G. / Mourier, G. / Servent, D. | ||||||
![]() | ![]() Title: Ancestral protein resurrection and engineering opportunities of the mamba aminergic toxins. Authors: Blanchet, G. / Alili, D. / Protte, A. / Upert, G. / Gilles, N. / Tepshi, L. / Stura, E.A. / Mourier, G. / Servent, D. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 45.3 KB | Display | ![]() |
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PDB format | ![]() | 31.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4iyeS S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 7255.345 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: Putative ancetral mamba toxin, Residues 1 to 6 (LEU THR CYS VAL LYS SER ) match to UNP Q8QGR0 NXM11_DENAN 22 to 28, Residues 7 to 11 (LYS SER ILE PHE GLY ) match to UNP P85092 TXAD1_DENAN 7 ...Details: Putative ancetral mamba toxin, Residues 1 to 6 (LEU THR CYS VAL LYS SER ) match to UNP Q8QGR0 NXM11_DENAN 22 to 28, Residues 7 to 11 (LYS SER ILE PHE GLY ) match to UNP P85092 TXAD1_DENAN 7 to 11, Residues 12 to 17 (VAL THR THR GLU ASP CYS ) match to UNP P18328 TXM2_DENAN 12 to 17, Residues 18 to 26 (PRO ASP GLY GLN ASN LEU CYS PHE LYS ) match to UNP P81030 TXM1_DENAN 18 to 26, Residues 27 to 31 (ARG ARG HIS TYR ILE ) match to UNP P86419 3SI1B_DENAN 27 to 31, Residues 32 to 34 (VAL PRO LYS ) match to UNP P85092 TXAD1_DENAN 32 to 34, Residues 35 to 37 (MET TYR ASP ) match to UNP Q8QGR0 NXM11_DENAN 56 to 58, Residues 38 to 48 (SER THR ARG GLY CYS ALA ALA THR CYS PRO ILE ) match to UNP P85092 TXAD1_DENAN 38 to 48, Residues 49 to 50 (ALA GLU ) match to UNP Q8QGR0 NXM11_DENAN 61 to 62, Residues 51 to 54 (ASN ARG ASP VAL ) match to UNP P82462 3SUC1_NAJKA 51 to 54, Residues 55 to 58 (ILE HIS CYS CYS ) match to UNP P85092 TXAD1_DENAN 55 to 58, Residues 59 to 62 (GLY THR ASP LYS ) match to UNP P18328 TXM2_DENAN 59 to 62, Residues 63 to 65 (CYS ASN GLU ) match to UNP P85092 TXAD1_DENAN 63 to 65, Source: (synth.) ![]() References: UniProt: P85092*PLUS |
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-Non-polymers , 5 types, 94 molecules ![](data/chem/img/PGO.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/YVR.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/YVR.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-PGO / | ||||
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#3: Chemical | ChemComp-EDO / | ||||
#4: Chemical | ChemComp-SO4 / #5: Chemical | ChemComp-YVR / | #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.25 Å3/Da / Density % sol: 45.44 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: Protein: lyophilized synthetic toxin at 5 mg/mL in 1 M Na Acetate pH 5.5. Precipitant: 1.9 M ammonium sulfate, 4 % MPD, 2 % 1,4-dioxane, 2 % gamma-valerolactone, 0.132 M sodium citrate, pH 5. ...Details: Protein: lyophilized synthetic toxin at 5 mg/mL in 1 M Na Acetate pH 5.5. Precipitant: 1.9 M ammonium sulfate, 4 % MPD, 2 % 1,4-dioxane, 2 % gamma-valerolactone, 0.132 M sodium citrate, pH 5.5. Cryoprotectant: 80% saturated lithium sulfate, 10% Dioxane, 10% gamma-valerolactone PH range: 5.5 / Temp details: Cooled incubator |
-Data collection
Diffraction | Mean temperature: 100 K / Ambient temp details: cryostream |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jan 29, 2015 Details: Compound Refractive Lens Fully automatic data collection |
Radiation | Monochromator: diamond beam splitter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.965 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→35.556 Å / Num. obs: 11687 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 8.3 % / CC1/2: 0.999 / Rmerge(I) obs: 0.111 / Rsym value: 0.104 / Net I/σ(I): 12.24 |
Reflection shell | Resolution: 1.8→1.91 Å / Redundancy: 8.2 % / Rmerge(I) obs: 1.53 / Mean I/σ(I) obs: 1.16 / CC1/2: 0.719 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4IYE Resolution: 1.801→35.556 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 30.62 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.801→35.556 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 20.7852 Å / Origin y: -8.891 Å / Origin z: -8.7359 Å
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Refinement TLS group | Selection details: all |