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- PDB-5do6: Crystal structure of Dendroaspis polylepis venom mambalgin-1 T23A... -

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Basic information

Entry
Database: PDB / ID: 5do6
TitleCrystal structure of Dendroaspis polylepis venom mambalgin-1 T23A mutant
ComponentsMambalgin-1
KeywordsTOXIN / Acid Sensing Ion Channels / Pain suppression Drug / Elapid Venom polypeptide
Function / homology
Function and homology information


ion channel regulator activity / toxin activity / extracellular region
Similarity search - Function
: / Snake toxin cobra-type / Snake three-finger toxin / CD59 / CD59 / Snake toxin-like superfamily / Ribbon / Mainly Beta
Similarity search - Domain/homology
IODIDE ION / S-1,2-PROPANEDIOL / Mambalgin-1
Similarity search - Component
Biological speciesDendroaspis polylepis polylepis (black mamba)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.697 Å
AuthorsStura, E.A. / Tepshi, L. / Kessler, P. / Gilles, M. / Servent, D.
Citation
Journal: J.Biol.Chem. / Year: 2016
Title: Mambalgin-1 Pain-relieving Peptide, Stepwise Solid-phase Synthesis, Crystal Structure, and Functional Domain for Acid-sensing Ion Channel 1a Inhibition.
Authors: Mourier, G. / Salinas, M. / Kessler, P. / Stura, E.A. / Leblanc, M. / Tepshi, L. / Besson, T. / Diochot, S. / Baron, A. / Douguet, D. / Lingueglia, E. / Servent, D.
#1: Journal: J Synchrotron Radiat / Year: 2017
Title: Comparison of helical scan and standard rotation methods in single-crystal X-ray data collection strategies.
Authors: Polsinelli, I. / Savko, M. / Rouanet-Mehouas, C. / Ciccone, L. / Nencetti, S. / Orlandini, E. / Stura, E.A. / Shepard, W.
History
DepositionSep 10, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Dec 30, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 17, 2016Group: Database references
Revision 1.2Jan 25, 2017Group: Database references
Revision 1.3Oct 23, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Mambalgin-1
B: Mambalgin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,8629
Polymers13,0892
Non-polymers7737
Water2,972165
1
A: Mambalgin-1
B: Mambalgin-1
hetero molecules

A: Mambalgin-1
B: Mambalgin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,72418
Polymers26,1784
Non-polymers1,54514
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Buried area6410 Å2
ΔGint-27 kcal/mol
Surface area12520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.900, 100.990, 53.480
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-266-

HOH

21B-239-

HOH

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Components

#1: Protein Mambalgin-1 / Mamb-1 / Pi-Dp1


Mass: 6544.618 Da / Num. of mol.: 2 / Fragment: UNP residues 22-78 / Mutation: T23A / Source method: obtained synthetically / Details: T23A mutant
Source: (synth.) Dendroaspis polylepis polylepis (black mamba)
References: UniProt: P0DKR6
#2: Chemical
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: I
#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-PGO / S-1,2-PROPANEDIOL


Mass: 76.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 165 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.88 Å3/Da / Density % sol: 57.34 % / Description: Prismatic crystals
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.6
Details: Protein: redissolved from lyophilized at 5mg/ml mamb-1-T23A in 50mM Na Acetate, pH 5.5. Precipitant: 21.6% PEG600, 3.6% PEG 20K 0.18M mixed L-malic acid, MES, Tris (pH4) and mixed sodium ...Details: Protein: redissolved from lyophilized at 5mg/ml mamb-1-T23A in 50mM Na Acetate, pH 5.5. Precipitant: 21.6% PEG600, 3.6% PEG 20K 0.18M mixed L-malic acid, MES, Tris (pH4) and mixed sodium Malonate, imidazole, boric acid(pH10) in the ratio 40:60. Cryoprotectant: 30% MPEG 550, 40% CryoProtX cryomix9, 10% NaAc pH 6.5, 0.1M potassium iodide soaked for 1 min.
PH range: 5.5 - 7.6 / Temp details: cooled incubator

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: N2 cryostat - Helical scan
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.9801 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 3, 2015 / Details: X-ray centering - Helical scan
RadiationMonochromator: [111] Si Cut monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9801 Å / Relative weight: 1
ReflectionResolution: 1.697→37 Å / Num. all: 16719 / Num. obs: 31543 / % possible obs: 97.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.1 % / Rmerge(I) obs: 0.061 / Rsym value: 0.057 / Net I/σ(I): 21.83
Reflection shellResolution: 1.697→1.74 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.408 / Mean I/σ(I) obs: 4.64 / % possible all: 78.7

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XSCALEdata scaling
PHENIXAutoSolphasing
Cootmodel building
RefinementMethod to determine structure: SAD / Resolution: 1.697→27.95 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 21.25 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2048 837 5.01 %Random
Rwork0.1715 ---
obs0.1731 16719 97.69 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.697→27.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms898 0 14 165 1077
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061033
X-RAY DIFFRACTIONf_angle_d1.0171382
X-RAY DIFFRACTIONf_dihedral_angle_d12.35406
X-RAY DIFFRACTIONf_chiral_restr0.043142
X-RAY DIFFRACTIONf_plane_restr0.005187
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6974-1.80380.25241220.20422302X-RAY DIFFRACTION87
1.8038-1.9430.23761390.18292650X-RAY DIFFRACTION100
1.943-2.13850.21851420.16112700X-RAY DIFFRACTION100
2.1385-2.44780.19611410.16512683X-RAY DIFFRACTION100
2.4478-3.08330.2271440.17412725X-RAY DIFFRACTION100
3.0833-27.95380.17881490.16862822X-RAY DIFFRACTION100

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