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- PDB-7pud: Bryoporin - actinoporin from moss Physcomitrium patens -

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Basic information

Entry
Database: PDB / ID: 7pud
TitleBryoporin - actinoporin from moss Physcomitrium patens
ComponentsBryoporin
KeywordsPLANT PROTEIN / Actinoporin / Membrane-binding / pore-formation / moss
Function / homologySea anemone actinoporin-like / Sea anemone cytotoxic protein / Cytolysin/lectin / pore complex assembly / hemolysis in another organism / channel activity / pore complex / monoatomic cation transport / Bryoporin
Function and homology information
Biological speciesPhyscomitrium patens (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.25 Å
AuthorsSolinc, G. / Anderluh, G. / Podobnik, M.
Funding support Slovenia, 1items
OrganizationGrant numberCountry
Slovenian Research AgencyP1-0391 Slovenia
CitationJournal: J.Biol.Chem. / Year: 2022
Title: Pore-forming moss protein bryoporin is structurally and mechanistically related to actinoporins from evolutionarily distant cnidarians.
Authors: Solinc, G. / Svigelj, T. / Omersa, N. / Snoj, T. / Pirc, K. / Znidarsic, N. / Yamaji-Hasegawa, A. / Kobayashi, T. / Anderluh, G. / Podobnik, M.
History
DepositionSep 29, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 28, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 5, 2022Group: Database references / Category: citation
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Oct 12, 2022Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.3Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Bryoporin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,42811
Polymers21,4231
Non-polymers1,00510
Water3,279182
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1830 Å2
ΔGint-117 kcal/mol
Surface area8160 Å2
Unit cell
Length a, b, c (Å)37.918, 54.497, 81.967
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Space group name HallP22ab(z,x,y)
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y+1/2,-z+1/2
#4: -x,-y+1/2,z+1/2

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Components

#1: Protein Bryoporin / PpBP / Physcomitrin


Mass: 21422.822 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Physcomitrium patens (plant) / Gene: PHYPADRAFT_61094 / Plasmid: pET24a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q5UCA8
#2: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 182 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 1.97 Å3/Da / Density % sol: 37.6 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / Details: ammonium sulphate, NaCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Mar 10, 2015
Details: a vertical collimating mirror, a double-crystal Si(111) monochromator, a bendable focussing mirror
RadiationMonochromator: a vertical collimating mirror, a double-crystal Si(111) monochromator, a bendable focussing mirror
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.25→34.41 Å / Num. obs: 45262 / % possible obs: 94.78 % / Redundancy: 6 % / Biso Wilson estimate: 9.98 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.04733 / Rpim(I) all: 0.02163 / Rrim(I) all: 0.05227 / Net I/av σ(I): 21.01 / Net I/σ(I): 21.01
Reflection shellResolution: 1.251→1.295 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.4168 / Mean I/σ(I) obs: 3.6 / Num. unique obs: 3873 / CC1/2: 0.933 / CC star: 0.982 / Rpim(I) all: 0.2023 / Rrim(I) all: 0.465 / % possible all: 82.39

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
Coot0.9.4model building
PHENIX1.19.2_4158model building
XSCALEdata scaling
PHASER1.18.2_3874phasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3VWI

3vwi


Resolution: 1.25→34.41 Å / SU ML: 0.1354 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 23.7195
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2282 1965 4.4 %
Rwork0.2095 42664 -
obs0.2103 44629 93.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 14.67 Å2
Refinement stepCycle: LAST / Resolution: 1.25→34.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1381 0 56 182 1619
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00651544
X-RAY DIFFRACTIONf_angle_d0.94622116
X-RAY DIFFRACTIONf_chiral_restr0.0918220
X-RAY DIFFRACTIONf_plane_restr0.0061270
X-RAY DIFFRACTIONf_dihedral_angle_d10.6637217
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.25-1.280.34091280.28732777X-RAY DIFFRACTION86.51
1.28-1.320.539990.53652120X-RAY DIFFRACTION66.02
1.32-1.360.25311420.23763076X-RAY DIFFRACTION94.95
1.36-1.40.24381440.18913112X-RAY DIFFRACTION97.75
1.4-1.450.30761360.2512937X-RAY DIFFRACTION90.92
1.45-1.510.29491280.33632819X-RAY DIFFRACTION87.16
1.51-1.580.23031470.18743195X-RAY DIFFRACTION99.02
1.58-1.660.18781490.17253220X-RAY DIFFRACTION99.53
1.66-1.760.21321490.18123216X-RAY DIFFRACTION99.67
1.76-1.90.211510.19183262X-RAY DIFFRACTION99.39
1.9-2.090.23541360.23123019X-RAY DIFFRACTION92.77
2.09-2.390.23371440.21443154X-RAY DIFFRACTION95.43
2.39-3.010.21661540.18473322X-RAY DIFFRACTION99.83
3.01-32.750.18661580.17673435X-RAY DIFFRACTION98.76

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