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- PDB-8vo1: Pathogenesis related 10-10 C155S mutant -

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Basic information

Entry
Database: PDB / ID: 8vo1
TitlePathogenesis related 10-10 C155S mutant
ComponentsPathogenesis related 10-10 C155S 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: 1.8 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 C155S mutant


Theoretical massNumber of molelcules
Total (without water)17,6101
Polymers17,6101
Non-polymers00
Water1,56787
1
A: Pathogenesis related 10-10 C155S mutant

A: Pathogenesis related 10-10 C155S 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-8 kcal/mol
Surface area16120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.400, 70.836, 92.205
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 C155S mutant


Mass: 17609.830 Da / Num. of mol.: 1 / Mutation: C155S
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.: 87 / 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: 2.24 Å3/Da / Density % sol: 45.19 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop
Details: 23% 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: 1.8→36.7 Å / Num. obs: 15041 / % possible obs: 99.7 % / Redundancy: 10.9 % / Biso Wilson estimate: 29.58 Å2 / CC1/2: 1 / Rsym value: 0.05 / Net I/σ(I): 29.15
Reflection shellResolution: 1.8→1.84 Å / Mean I/σ(I) obs: 1.9 / Num. unique obs: 1088 / CC1/2: 0.802 / Rsym value: 1.316

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
Blu-Icedata collection
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→36.67 Å / SU ML: 0.2042 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.9618
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2328 1500 10 %
Rwork0.2035 13506 -
obs0.2064 15006 99.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 38.61 Å2
Refinement stepCycle: LAST / Resolution: 1.8→36.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1150 0 0 87 1237
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00771197
X-RAY DIFFRACTIONf_angle_d1.01771627
X-RAY DIFFRACTIONf_chiral_restr0.0703185
X-RAY DIFFRACTIONf_plane_restr0.0061207
X-RAY DIFFRACTIONf_dihedral_angle_d7.1848156
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.860.33071330.28611197X-RAY DIFFRACTION98.88
1.86-1.920.28581320.24231188X-RAY DIFFRACTION99.85
1.92-20.28081360.23591218X-RAY DIFFRACTION99.71
2-2.090.26641340.21891211X-RAY DIFFRACTION99.78
2.09-2.20.26961350.21541222X-RAY DIFFRACTION99.41
2.2-2.340.27671340.2091202X-RAY DIFFRACTION99.7
2.34-2.520.26741390.21781248X-RAY DIFFRACTION99.93
2.52-2.770.27991330.23571210X-RAY DIFFRACTION99.7
2.78-3.180.25911390.22071242X-RAY DIFFRACTION99.93
3.18-40.20591390.18671256X-RAY DIFFRACTION99.71
4-36.670.18271460.17551312X-RAY DIFFRACTION99.59

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