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- PDB-5du1: Crystal structure of Dendroaspis polylepis mambalgin-1 wild-type ... -

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Basic information

Entry
Database: PDB / ID: 5du1
TitleCrystal structure of Dendroaspis polylepis mambalgin-1 wild-type in P21 space group.
ComponentsMambalgin-1
KeywordsTOXIN / Acid Sensing Ion Channels / Elapid Venoms / analgesic polypeptide
Function / homology
Function and homology information


ion channel regulator activity / toxin activity / extracellular region
Similarity search - Function
Snake three-finger toxin / : / Snake toxin cobra-type / CD59 / CD59 / Snake toxin-like superfamily / Ribbon / Mainly Beta
Similarity search - Domain/homology
Biological speciesDendroaspis polylepis polylepis (black mamba)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsStura, E.A. / Tepshi, L. / Mourier, G. / Kessler, P. / Servent, D.
CitationJournal: 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.
History
DepositionSep 18, 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 10, 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Mambalgin-1
B: Mambalgin-1
C: Mambalgin-1
D: Mambalgin-1


Theoretical massNumber of molelcules
Total (without water)26,2994
Polymers26,2994
Non-polymers00
Water3,531196
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4860 Å2
ΔGint-28 kcal/mol
Surface area12640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.030, 50.240, 46.880
Angle α, β, γ (deg.)90.00, 93.38, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: LEU / Beg label comp-ID: LEU / End auth comp-ID: LYS / End label comp-ID: LYS / Refine code: _ / Auth seq-ID: 1 - 57 / Label seq-ID: 1 - 57

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21BB
12AA
22CC
13AA
23DD
14BB
24CC
15BB
25DD
16CC
26DD

NCS ensembles :
ID
1
2
3
4
5
6

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Components

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


Mass: 6574.644 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Details: wild-type polypeptide found in the venom
Source: (natural) Dendroaspis polylepis polylepis (black mamba)
References: UniProt: P0DKR6
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 196 / 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: 1.74 Å3/Da / Density % sol: 29.41 % / Description: prismatic
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6
Details: protein: 5 mg/mL in 0.550 M Na Acetate pH 5.5 precipitant: 18% PEG4K, 3% MPD, 3% 1,4-dioxane, .188 M Imidazole Malate, pH 6 cryoprotectant:: CrySol-SM5, 30% PEG 600, 0.1 M mixed (Na acetate, ADA, Bicine), pH 7.5
PH range: 6-7.5 / Temp details: cooled incubator

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Data collection

DiffractionMean temperature: 100 K
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→46.796 Å / Num. all: 15969 / Num. obs: 15969 / % possible obs: 93.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 2.7 % / Rmerge(I) obs: 0.063 / Rsym value: 0.052 / Net I/σ(I): 13.77
Reflection shellResolution: 1.8→1.91 Å / Redundancy: 2.77 % / Rmerge(I) obs: 0.257 / Mean I/σ(I) obs: 4.35 / % possible all: 84.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0123refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5DO6

5do6


Resolution: 1.8→38.96 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.936 / SU B: 3.832 / SU ML: 0.115 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.174 / ESU R Free: 0.153 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22433 807 5 %RANDOM
Rwork0.17406 ---
obs0.17662 15332 95.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.705 Å2
Baniso -1Baniso -2Baniso -3
1-3.11 Å2-0 Å20.22 Å2
2---1.22 Å2-0 Å2
3----1.9 Å2
Refinement stepCycle: 1 / Resolution: 1.8→38.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1804 0 0 196 2000
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0191906
X-RAY DIFFRACTIONr_bond_other_d0.0130.021765
X-RAY DIFFRACTIONr_angle_refined_deg2.0651.9452559
X-RAY DIFFRACTIONr_angle_other_deg2.37534091
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.9975235
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.85523.48886
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.15915377
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.0291514
X-RAY DIFFRACTIONr_chiral_restr0.1030.2266
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.022160
X-RAY DIFFRACTIONr_gen_planes_other0.0110.02462
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.6962.406937
X-RAY DIFFRACTIONr_mcbond_other2.6762.402936
X-RAY DIFFRACTIONr_mcangle_it4.1233.5861173
X-RAY DIFFRACTIONr_mcangle_other4.1253.5881174
X-RAY DIFFRACTIONr_scbond_it3.7232.894969
X-RAY DIFFRACTIONr_scbond_other3.7152.895969
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.764.1511386
X-RAY DIFFRACTIONr_long_range_B_refined9.46220.8782177
X-RAY DIFFRACTIONr_long_range_B_other9.44620.5152137
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A49720.23
12B49720.23
21A51640.21
22C51640.21
31A50060.25
32D50060.25
41B54280.19
42C54280.19
51B49660.24
52D49660.24
61C49320.24
62D49320.24
LS refinement shellResolution: 1.799→1.846 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.387 42 -
Rwork0.255 799 -
obs--67.93 %

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