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- PDB-5mg9: Putative Ancestral Mamba toxin 1 (AncTx1-W28R/I38S) -

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Basic information

Entry
Database: PDB / ID: 5mg9
TitlePutative Ancestral Mamba toxin 1 (AncTx1-W28R/I38S)
ComponentsAncTx1-W28R/I38S
KeywordsTOXIN / Ancestral mamba snake toxin / three-finger fold / Ancestral toxin resurrection and engineering / aminergic toxin
Function / homology
Function and homology information


toxin activity / extracellular region
Similarity search - Function
Snake three-finger toxin / Snake toxins signature. / Snake toxin, conserved site / CD59 / CD59 / Snake toxin-like superfamily / Ribbon / Mainly Beta
Similarity search - Domain/homology
S-1,2-PROPANEDIOL / gamma-Valerolactone / Toxin AdTx1
Similarity search - Component
Biological speciesDendroaspis angusticeps (eastern green mamba)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.801 Å
AuthorsStura, E.A. / Tepshi, L. / Blanchet, G. / Mourier, G. / Servent, D.
CitationJournal: Sci Rep / Year: 2017
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
DepositionNov 21, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 3, 2017Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation_author.name
Revision 1.2Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: AncTx1-W28R/I38S
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,8788
Polymers7,2551
Non-polymers6237
Water1,56787
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area660 Å2
ΔGint-13 kcal/mol
Surface area4760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.057, 41.057, 67.118
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein AncTx1-W28R/I38S / Toxin AdTx1 / Rho-elapitoxin-Da1a / Rho-EPTX-Da1a


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.) Dendroaspis angusticeps (eastern green mamba)
References: UniProt: P85092*PLUS

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Non-polymers , 5 types, 94 molecules

#2: Chemical ChemComp-PGO / S-1,2-PROPANEDIOL


Mass: 76.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O2
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-YVR / gamma-Valerolactone


Mass: 100.116 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H8O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 87 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.25 Å3/Da / Density % sol: 45.44 %
Crystal growTemperature: 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

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: cryostream
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.965 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jan 29, 2015
Details: Compound Refractive Lens Fully automatic data collection
RadiationMonochromator: diamond beam splitter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.965 Å / Relative weight: 1
ReflectionResolution: 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 shellResolution: 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

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4IYE

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
RfactorNum. reflection% reflection
Rfree0.2365 823 7.04 %
Rwork0.2032 --
obs0.2056 11685 99.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.801→35.556 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms500 0 36 87 623
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.004551
X-RAY DIFFRACTIONf_angle_d0.809746
X-RAY DIFFRACTIONf_dihedral_angle_d14.383339
X-RAY DIFFRACTIONf_chiral_restr0.04780
X-RAY DIFFRACTIONf_plane_restr0.00493
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8006-1.91340.41171380.38691785X-RAY DIFFRACTION99
1.9134-2.06110.29921380.29281826X-RAY DIFFRACTION100
2.0611-2.26850.27151280.23611812X-RAY DIFFRACTION100
2.2685-2.59660.22441430.21271802X-RAY DIFFRACTION100
2.5966-3.27110.22971360.1991809X-RAY DIFFRACTION100
3.2711-35.56330.20591400.16171828X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 20.7852 Å / Origin y: -8.891 Å / Origin z: -8.7359 Å
111213212223313233
T0.2677 Å20.0655 Å2-0.0015 Å2-0.2705 Å20.0205 Å2--0.2316 Å2
L0.9453 °2-0.0395 °2-0.6787 °2-0.9564 °20.5933 °2--0.8977 °2
S-0.0078 Å °0.0458 Å °0.1231 Å °0.0705 Å °0.0276 Å °0.0113 Å °-0.158 Å °-0.1611 Å °0.0001 Å °
Refinement TLS groupSelection details: all

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