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- PDB-7uqn: Pathogenesis related 10-10 noscapine complex -

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Basic information

Entry
Database: PDB / ID: 7uqn
TitlePathogenesis related 10-10 noscapine complex
ComponentsPathogenesis Related 10-10 protein
KeywordsBIOSYNTHETIC PROTEIN / binding protein / alkaloids / opium poppy
Function / homologynoscapine
Function and homology information
Biological speciesPapaver somniferum (opium poppy)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Pathogenesis Related 10-10 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,0392
Polymers17,6261
Non-polymers4131
Water1,56787
1
A: Pathogenesis Related 10-10 protein
hetero molecules

A: Pathogenesis Related 10-10 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,0794
Polymers35,2522
Non-polymers8272
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area1510 Å2
ΔGint-9 kcal/mol
Surface area15770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.871, 71.565, 91.651
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 protein


Mass: 17625.895 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Papaver somniferum (opium poppy) / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-08N / noscapine / (3S)-6,7-dimethoxy-3-[(5R)-4-methoxy-6-methyl-5,6,7,8-tetrahydro-2H-[1,3]dioxolo[4,5-g]isoquinolin-5-yl]-2-benzofuran-1(3H)-one


Mass: 413.421 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H23NO7 / Feature type: SUBJECT OF INVESTIGATION / Comment: alkaloid*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 87 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 45.89 %
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: Feb 25, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.7→36.94 Å / Num. obs: 17557 / % possible obs: 96.8 % / Redundancy: 12.4 % / Biso Wilson estimate: 25.07 Å2 / CC1/2: 1 / Net I/σ(I): 37.17
Reflection shellResolution: 1.7→1.75 Å / Num. unique obs: 1021 / CC1/2: 0.969

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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
Starting model: 7UQL

7uql


Resolution: 1.7→36.94 Å / SU ML: 0.1893 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.5376
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2345 1742 9.98 %
Rwork0.1921 15710 -
obs0.1964 17452 96.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 38.83 Å2
Refinement stepCycle: LAST / Resolution: 1.7→36.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1167 0 30 87 1284
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01331257
X-RAY DIFFRACTIONf_angle_d1.50721716
X-RAY DIFFRACTIONf_chiral_restr0.0897189
X-RAY DIFFRACTIONf_plane_restr0.0086218
X-RAY DIFFRACTIONf_dihedral_angle_d18.8263484
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.750.31641180.2361059X-RAY DIFFRACTION78.1
1.75-1.810.27831400.211256X-RAY DIFFRACTION93.88
1.81-1.870.30131450.21261309X-RAY DIFFRACTION99.18
1.87-1.940.28621420.23071298X-RAY DIFFRACTION96.45
1.94-2.030.26661480.22331324X-RAY DIFFRACTION98.99
2.03-2.140.26811440.20741286X-RAY DIFFRACTION96.75
2.14-2.270.24371480.21011345X-RAY DIFFRACTION98.35
2.27-2.450.27981480.211341X-RAY DIFFRACTION99.6
2.45-2.70.25261490.20891336X-RAY DIFFRACTION98.47
2.7-3.090.23321520.20321364X-RAY DIFFRACTION99.87
3.09-3.890.2321470.17391357X-RAY DIFFRACTION98.17
3.89-36.940.18421610.1681435X-RAY DIFFRACTION98.95

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