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- PDB-8vo2: Pathogenesis related 10-10 C59S mutant -

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Basic information

Entry
Database: PDB / ID: 8vo2
TitlePathogenesis related 10-10 C59S mutant
ComponentsPathogenesis related 10-10 C59S mutant
KeywordsPLANT PROTEIN / Opium poppy / papaver somniferum / benzylisoquinoline alkaloid / binding protein / latex / pathogenesis related protein / major latex protein
Biological speciesPapaver somniferum (opium poppy)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsCarr, S.C. / Facchini, P.J. / 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


Theoretical massNumber of molelcules
Total (without water)17,6101
Polymers17,6101
Non-polymers00
Water2,468137
1
A: Pathogenesis related 10-10 C59S mutant

A: Pathogenesis related 10-10 C59S mutant


Theoretical massNumber of molelcules
Total (without water)35,2202
Polymers35,2202
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area1530 Å2
ΔGint-7 kcal/mol
Surface area16250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.870, 71.087, 91.858
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 137 / Source method: isolated from a natural source / Formula: H2O
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: 2.27 Å3/Da / Density % sol: 45.7 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop
Details: 18% polyethylene glycol 3350, 0.1M Bis-Tris pH 5.5, 0.2M sodium chloride
PH range: 5.5

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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→36.88 Å / Num. obs: 25883 / % possible obs: 99.2 % / Redundancy: 10.3 % / Biso Wilson estimate: 21.8 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.046 / Net I/σ(I): 25.32
Reflection shellResolution: 1.5→1.54 Å / Mean I/σ(I) obs: 1.76 / Num. unique obs: 1804 / CC1/2: 0.773 / Rsym value: 1.101

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHENIX1.18.2-3874refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→36.88 Å / SU ML: 0.1938 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.5008
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2377 1999 7.73 %
Rwork0.203 23849 -
obs0.2056 25848 99.21 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 30.39 Å2
Refinement stepCycle: LAST / Resolution: 1.5→36.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1169 0 0 137 1306
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00611211
X-RAY DIFFRACTIONf_angle_d0.8571647
X-RAY DIFFRACTIONf_chiral_restr0.0798187
X-RAY DIFFRACTIONf_plane_restr0.0058211
X-RAY DIFFRACTIONf_dihedral_angle_d13.7418436
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.540.29351340.29731608X-RAY DIFFRACTION93.61
1.54-1.580.28021370.25911627X-RAY DIFFRACTION98.49
1.58-1.620.2981430.2551705X-RAY DIFFRACTION99.95
1.62-1.680.29041410.2311695X-RAY DIFFRACTION99.89
1.68-1.740.28981430.22691700X-RAY DIFFRACTION99.84
1.74-1.810.25411430.2251702X-RAY DIFFRACTION99.78
1.81-1.890.24651420.22071696X-RAY DIFFRACTION99.73
1.89-1.990.26291420.23791693X-RAY DIFFRACTION99.73
1.99-2.110.27041430.20391699X-RAY DIFFRACTION99.73
2.11-2.280.24461430.19681717X-RAY DIFFRACTION99.41
2.28-2.510.24441430.20531697X-RAY DIFFRACTION99.84
2.51-2.870.23021460.21361745X-RAY DIFFRACTION99.68
2.87-3.610.2281460.19081752X-RAY DIFFRACTION99.79
3.61-36.880.20881530.18121813X-RAY DIFFRACTION99.49

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