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- PDB-8vo3: Pathogenesis related 10-10 C59S mutant papaverine complex -

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Basic information

Entry
Database: PDB / ID: 8vo3
TitlePathogenesis related 10-10 C59S mutant papaverine complex
ComponentsPathogenesis related 10-10 C59S mutant
KeywordsPLANT PROTEIN / Opium poppy / papaver somniferum / benzylisoquinoline alkaloid / binding protein / latex / pathogenesis related protein / major latex protein
Function / homology1-(3,4-DIMETHOXYBENZYL)-6,7-DIMETHOXYISOQUINOLINE
Function and homology information
Biological speciesPapaver somniferum (opium poppy)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsCarr, S.C. / Ng, K.K.S.
Funding support Canada, 1items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada)05728 Canada
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2024
Title: Structural analysis of a ligand-triggered intermolecular disulfide switch in a major latex protein from opium poppy.
Authors: Carr, S.C. / Facchini, P.J. / Ng, K.K.S.
History
DepositionJan 14, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 23, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Pathogenesis related 10-10 C59S mutant
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,9492
Polymers17,6101
Non-polymers3391
Water2,072115
1
A: Pathogenesis related 10-10 C59S mutant
hetero molecules

A: Pathogenesis related 10-10 C59S mutant
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,8984
Polymers35,2202
Non-polymers6792
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area1560 Å2
ΔGint-8 kcal/mol
Surface area16020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.767, 71.491, 92.265
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2

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Components

#1: Protein Pathogenesis related 10-10 C59S mutant


Mass: 17609.828 Da / Num. of mol.: 1 / Mutation: C59S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Papaver somniferum (opium poppy) / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-EV1 / 1-(3,4-DIMETHOXYBENZYL)-6,7-DIMETHOXYISOQUINOLINE / Papaverine


Mass: 339.385 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H21NO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 115 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.28 Å3/Da / Density % sol: 46.13 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 5.1
Details: 1mM papaverine, 10% methanol, 17% (w/v) polyethylene glycol 3350, and 0.1M Bis-Tris pH 5.1

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 19, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.5→36.92 Å / Num. obs: 25890 / % possible obs: 98.2 % / Redundancy: 10.3 % / CC1/2: 1 / Rsym value: 0.029 / Net I/σ(I): 33.57
Reflection shellResolution: 1.5→1.54 Å / Mean I/σ(I) obs: 1.9 / Num. unique obs: 1632 / CC1/2: 0.808 / Rsym value: 1.057

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHENIX1.18.2_3874refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→36.92 Å / SU ML: 0.1984 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.4851
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.239 1999 7.73 %
Rwork0.2088 23858 -
obs0.2112 25857 98.14 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 35.82 Å2
Refinement stepCycle: LAST / Resolution: 1.5→36.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1144 0 25 115 1284
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00941219
X-RAY DIFFRACTIONf_angle_d1.1311657
X-RAY DIFFRACTIONf_chiral_restr0.1009184
X-RAY DIFFRACTIONf_plane_restr0.0063209
X-RAY DIFFRACTIONf_dihedral_angle_d14.0499432
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.530.31461210.30091454X-RAY DIFFRACTION84.45
1.54-1.580.27371360.27151603X-RAY DIFFRACTION94.72
1.58-1.620.27781430.26471713X-RAY DIFFRACTION99.04
1.62-1.680.30091410.25141698X-RAY DIFFRACTION99.73
1.68-1.740.34381450.25221726X-RAY DIFFRACTION99.68
1.74-1.80.29511440.23561718X-RAY DIFFRACTION99.47
1.8-1.890.25281440.23241712X-RAY DIFFRACTION99.57
1.89-1.990.25261420.24561708X-RAY DIFFRACTION99.62
1.99-2.110.24211440.21521711X-RAY DIFFRACTION99.68
2.11-2.270.27841460.2091743X-RAY DIFFRACTION99.58
2.27-2.50.23051440.21521717X-RAY DIFFRACTION99.84
2.5-2.860.25311470.21731760X-RAY DIFFRACTION99.53
2.86-3.610.22631480.19581764X-RAY DIFFRACTION99.58
3.61-36.920.21141540.18641831X-RAY DIFFRACTION99.25

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