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- PDB-7uqo: Pathogenesis related 10-10 (S)-tetrahydropapaverine complex -

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Basic information

Entry
Database: PDB / ID: 7uqo
TitlePathogenesis related 10-10 (S)-tetrahydropapaverine complex
ComponentsPathogenesis Related 10-10 protein
KeywordsBIOSYNTHETIC PROTEIN / binding protein / alkaloids / opium poppy / (S)-tetrahydropapaverine / tetrahydropapaverine
Function / homologySTART domain / Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 / 2-Layer Sandwich / Alpha Beta / Chem-S9T
Function and homology information
Biological speciesPapaver somniferum (opium poppy)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 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)17,9692
Polymers17,6261
Non-polymers3431
Water1,49583
1
A: Pathogenesis Related 10-10 protein
hetero molecules

A: Pathogenesis Related 10-10 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,9394
Polymers35,2522
Non-polymers6872
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area1590 Å2
ΔGint-8 kcal/mol
Surface area15330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.514, 71.586, 91.836
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-S9T / (1~{S})-1-[(3,4-dimethoxyphenyl)methyl]-6,7-dimethoxy-1,2,3,4-tetrahydroisoquinoline / S-Tetrahydropapaverine


Mass: 343.417 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H25NO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 83 / 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: 2.24 Å3/Da / Density % sol: 45.14 %
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: 1.75→36.8 Å / Num. obs: 16490 / % possible obs: 99.4 % / Redundancy: 8.6 % / Biso Wilson estimate: 27.67 Å2 / CC1/2: 0.999 / Net I/σ(I): 22.55
Reflection shellResolution: 1.75→1.8 Å / Num. unique obs: 1170 / CC1/2: 0.904

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Processing

Software
NameVersionClassification
Blu-Ice1.18.2_3874data collection
PHENIX1.18.2_3874refinement
Blu-Icedata collection
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7UQL

7uql


Resolution: 1.75→36.8 Å / SU ML: 0.1885 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.3591
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.231 1646 10.02 %
Rwork0.1978 14787 -
obs0.2012 16433 99.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 37.93 Å2
Refinement stepCycle: LAST / Resolution: 1.75→36.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1122 0 25 83 1230
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01571187
X-RAY DIFFRACTIONf_angle_d1.47751612
X-RAY DIFFRACTIONf_chiral_restr0.0935179
X-RAY DIFFRACTIONf_plane_restr0.0092202
X-RAY DIFFRACTIONf_dihedral_angle_d15.5114437
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.80.28811340.24671206X-RAY DIFFRACTION97.17
1.8-1.860.3161340.22391196X-RAY DIFFRACTION99.4
1.86-1.920.27211330.22611199X-RAY DIFFRACTION99.33
1.92-20.29591370.22181227X-RAY DIFFRACTION99.56
2-2.090.26431340.21781213X-RAY DIFFRACTION99.48
2.09-2.20.24571380.2041234X-RAY DIFFRACTION99.42
2.2-2.340.26671350.20911209X-RAY DIFFRACTION99.26
2.34-2.520.23261380.2041245X-RAY DIFFRACTION99.71
2.52-2.770.25661380.22441230X-RAY DIFFRACTION99.71
2.78-3.180.22651380.20231244X-RAY DIFFRACTION99.35
3.18-40.20331400.181267X-RAY DIFFRACTION99.65
4-36.80.20641470.18171317X-RAY DIFFRACTION99.19

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