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- PDB-7uql: Pathogenesis related 10-10 app from -

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Basic information

Entry
Database: PDB / ID: 7uql
TitlePathogenesis related 10-10 app from
ComponentsPathogenesis Related 10-10 protein
KeywordsBIOSYNTHETIC PROTEIN / binding protein / alkaloids / opium poppy
Function / homologySTART domain / Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 / 2-Layer Sandwich / Alpha Beta
Function and homology information
Biological speciesPapaver somniferum (opium poppy)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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: Nat Commun / Year: 2022
Title: Alkaloid binding to opium poppy major latex proteins triggers structural modification and functional aggregation.
Authors: Ozber, N. / Carr, S.C. / Morris, J.S. / Liang, S. / Watkins, J.L. / Caldo, K.M. / Hagel, J.M. / Ng, K.K.S. / Facchini, P.J.
History
DepositionApr 19, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 1, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Pathogenesis Related 10-10 protein
B: Pathogenesis Related 10-10 protein


Theoretical massNumber of molelcules
Total (without water)35,2522
Polymers35,2522
Non-polymers00
Water2,072115
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: conserved dimer interface with related proteins. Non-reducing SDS-PAGE gel electrophoresis supports the presence of disulfide linkages.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1560 Å2
ΔGint-8 kcal/mol
Surface area14910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.175, 92.547, 52.858
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z

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Components

#1: Protein Pathogenesis Related 10-10 protein


Mass: 17625.895 Da / Num. of mol.: 2
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.: 115 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.41 Å3/Da / Density % sol: 49.03 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: PEG 3350, Bis-Tris pH 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: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 3, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.9→38.6 Å / Num. obs: 27479 / % possible obs: 98.5 % / Redundancy: 8.1 % / Biso Wilson estimate: 34.66 Å2 / CC1/2: 1 / Net I/σ(I): 27.42
Reflection shellResolution: 1.9→1.95 Å / Num. unique obs: 1977 / CC1/2: 0.849

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHENIX1.18.2-3874refinement
Blu-Icedata collection
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6KA3

6ka3


Resolution: 1.9→35.09 Å / SU ML: 0.2218 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 29.1148
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2474 1996 7.27 %
Rwork0.2075 25447 -
obs0.2104 27443 98.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 46.91 Å2
Refinement stepCycle: LAST / Resolution: 1.9→35.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2225 0 0 115 2340
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00992289
X-RAY DIFFRACTIONf_angle_d0.94683102
X-RAY DIFFRACTIONf_chiral_restr0.0708348
X-RAY DIFFRACTIONf_plane_restr0.0061394
X-RAY DIFFRACTIONf_dihedral_angle_d22.8676818
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.950.35961370.31491742X-RAY DIFFRACTION97.11
1.95-20.33791390.28461785X-RAY DIFFRACTION98.16
2-2.060.34211400.25441771X-RAY DIFFRACTION97.55
2.06-2.120.30551390.24241798X-RAY DIFFRACTION98.58
2.12-2.20.26691430.21491808X-RAY DIFFRACTION98.44
2.2-2.290.27991390.21331767X-RAY DIFFRACTION98.55
2.29-2.390.29751420.22751808X-RAY DIFFRACTION98.73
2.39-2.520.23471410.21911800X-RAY DIFFRACTION97.44
2.52-2.680.24881420.22681819X-RAY DIFFRACTION99.39
2.68-2.880.32261440.241823X-RAY DIFFRACTION99.09
2.88-3.170.28141440.23211842X-RAY DIFFRACTION99.45
3.17-3.630.20941450.20431841X-RAY DIFFRACTION98.66
3.63-4.570.22721480.17751877X-RAY DIFFRACTION99.66
4.57-35.090.20791530.18141966X-RAY DIFFRACTION98.24

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