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- PDB-5m4v: X-ray structure of the mambaquaretin-1, a selective antagonist of... -

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Basic information

Entry
Database: PDB / ID: 5m4v
TitleX-ray structure of the mambaquaretin-1, a selective antagonist of the vasopressin type 2 receptor
ComponentsMambaquaretin-1
KeywordsTOXIN / Vasopressin antagonist / mamba venom / kunitz
Function / homology
Function and homology information


serine-type endopeptidase inhibitor activity / toxin activity / extracellular space
Similarity search - Function
: / Pancreatic trypsin inhibitor Kunitz domain / Factor Xa Inhibitor / Proteinase inhibitor I2, Kunitz, conserved site / Pancreatic trypsin inhibitor (Kunitz) family signature. / BPTI/Kunitz family of serine protease inhibitors. / Pancreatic trypsin inhibitor Kunitz domain / Kunitz/Bovine pancreatic trypsin inhibitor domain / Pancreatic trypsin inhibitor (Kunitz) family profile. / Pancreatic trypsin inhibitor Kunitz domain superfamily ...: / Pancreatic trypsin inhibitor Kunitz domain / Factor Xa Inhibitor / Proteinase inhibitor I2, Kunitz, conserved site / Pancreatic trypsin inhibitor (Kunitz) family signature. / BPTI/Kunitz family of serine protease inhibitors. / Pancreatic trypsin inhibitor Kunitz domain / Kunitz/Bovine pancreatic trypsin inhibitor domain / Pancreatic trypsin inhibitor (Kunitz) family profile. / Pancreatic trypsin inhibitor Kunitz domain superfamily / Few Secondary Structures / Irregular
Similarity search - Domain/homology
S-1,2-PROPANEDIOL / Mambaquaretin-1
Similarity search - Component
Biological speciesDendroaspis angusticeps (eastern green mamba)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.06 Å
AuthorsStura, E.A. / Vera, L. / Ciolek, J. / Mourier, G. / Gilles, N.
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017
Title: Green mamba peptide targets type-2 vasopressin receptor against polycystic kidney disease.
Authors: Ciolek, J. / Reinfrank, H. / Quinton, L. / Viengchareun, S. / Stura, E.A. / Vera, L. / Sigismeau, S. / Mouillac, B. / Orcel, H. / Peigneur, S. / Tytgat, J. / Droctove, L. / Beau, F. / ...Authors: Ciolek, J. / Reinfrank, H. / Quinton, L. / Viengchareun, S. / Stura, E.A. / Vera, L. / Sigismeau, S. / Mouillac, B. / Orcel, H. / Peigneur, S. / Tytgat, J. / Droctove, L. / Beau, F. / Nevoux, J. / Lombes, M. / Mourier, G. / De Pauw, E. / Servent, D. / Mendre, C. / Witzgall, R. / Gilles, N.
History
DepositionOct 19, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 3, 2017Provider: repository / Type: Initial release
Revision 1.1Jun 28, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jul 12, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.journal_id_ASTM ..._citation.country / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 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
Revision 1.4Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Mambaquaretin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,5634
Polymers6,4161
Non-polymers1473
Water1,874104
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area400 Å2
ΔGint-13 kcal/mol
Surface area3840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.840, 63.840, 32.960
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number90
Space group name H-MP4212
Components on special symmetry positions
IDModelComponents
11A-203-

HOH

21A-225-

HOH

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Components

#1: Protein Mambaquaretin-1


Mass: 6416.423 Da / Num. of mol.: 1 / Mutation: N18K, G19A / Source method: obtained synthetically
Source: (synth.) Dendroaspis angusticeps (eastern green mamba)
References: UniProt: A0A1Z0YU59*PLUS
#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-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 104 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsAt the time of annotation, Uniprot Id not available for this entry. Should map to Uniprot entry ...At the time of annotation, Uniprot Id not available for this entry. Should map to Uniprot entry C0HK15 with mutation at K15-A16.

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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: 2.62 Å3/Da / Density % sol: 53 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Protein: 7 mg/mL in 50mM sodium Acetate pH 5.5 Precipitant: 36% MPEG 2K, 0.45 M NaCl, 0.9 M KSCN, 0.1 M imidazole HCl, pH 7.5. Cryoprotectant: 5 % diethylene glycol, 5 % ethylene glycol, 5 % ...Details: Protein: 7 mg/mL in 50mM sodium Acetate pH 5.5 Precipitant: 36% MPEG 2K, 0.45 M NaCl, 0.9 M KSCN, 0.1 M imidazole HCl, pH 7.5. Cryoprotectant: 5 % diethylene glycol, 5 % ethylene glycol, 5 % MPD, 5 % glycerol, 5 % 1,2-propanediol, 5 % DMSO, 18% MPEG-2K, 100 mM linear mixed buffer 1: sodium acetate, ADA, and bicine, 20% at pH 4 and 80% at pH 10.
Temp details: cooled incubator

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: cryostream
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.976251 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 11, 2012 / Details: MIRRORS
RadiationMonochromator: CHANNEL-CUT SILICON MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976251 Å / Relative weight: 1
ReflectionResolution: 1.06→45.14 Å / Num. obs: 31490 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 23.75 % / Biso Wilson estimate: 16 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.08 / Rsym value: 0.078 / Net I/σ(I): 19.36
Reflection shellResolution: 1.06→1.09 Å / Redundancy: 19.16 % / Rmerge(I) obs: 2.84 / Mean I/σ(I) obs: 1.22 / CC1/2: 0.618 / % possible all: 99.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1B0C

1b0c


Resolution: 1.06→45.14 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.971 / SU B: 0.808 / SU ML: 0.017 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.023 / ESU R Free: 0.025 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.15574 1575 5 %RANDOM
Rwork0.13067 ---
obs0.13195 29915 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 19.648 Å2
Baniso -1Baniso -2Baniso -3
1-0.08 Å2-0 Å2-0 Å2
2--0.08 Å2-0 Å2
3----0.16 Å2
Refinement stepCycle: 1 / Resolution: 1.06→45.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms448 0 7 104 559
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0290.019564
X-RAY DIFFRACTIONr_bond_other_d0.0130.02521
X-RAY DIFFRACTIONr_angle_refined_deg2.7091.951765
X-RAY DIFFRACTIONr_angle_other_deg1.3831212
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.756574
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.48320.41724
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.8221599
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.121156
X-RAY DIFFRACTIONr_chiral_restr0.1340.271
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.021673
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02155
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_it1.8491.469275
X-RAY DIFFRACTIONr_mcbond_other1.6151.449274
X-RAY DIFFRACTIONr_mcangle_it2.0572.202356
X-RAY DIFFRACTIONr_mcangle_other2.0542.204357
X-RAY DIFFRACTIONr_scbond_it3.3771.872289
X-RAY DIFFRACTIONr_scbond_other3.3581.871289
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.3172.635410
X-RAY DIFFRACTIONr_long_range_B_refined6.38322.123734
X-RAY DIFFRACTIONr_long_range_B_other5.29920.051695
X-RAY DIFFRACTIONr_rigid_bond_restr6.63631085
X-RAY DIFFRACTIONr_sphericity_free32.975557
X-RAY DIFFRACTIONr_sphericity_bonded12.15251115
LS refinement shellResolution: 1.06→1.087 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.337 114 -
Rwork0.33 2156 -
obs--99.26 %

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