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- PDB-9x2o: X-ray structure of antiviral protein from Mirabilis jalapa -

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Basic information

Entry
Database: PDB / ID: 9x2o
TitleX-ray structure of antiviral protein from Mirabilis jalapa
ComponentsAntiviral protein MAP
KeywordsANTIVIRAL PROTEIN / Plant Toxin / RNA N-glycosidase
Function / homology
Function and homology information


rRNA N-glycosylase / rRNA N-glycosylase activity / toxin activity / defense response to virus / negative regulation of translation
Similarity search - Function
Ribosome-inactivating protein conserved site / Shiga/ricin ribosomal inactivating toxins active site signature. / Ribosome-inactivating protein type 1/2 / Ribosome-inactivating protein / Ribosome-inactivating protein, subdomain 1 / Ribosome-inactivating protein, subdomain 2 / Ribosome-inactivating protein superfamily / Ribosome inactivating protein
Similarity search - Domain/homology
Antiviral protein MAP
Similarity search - Component
Biological speciesMirabilis jalapa (garden four-o'clock)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsNishida, N. / Ninomiya, Y. / Yoshida, T. / Habuka, N. / Tsuge, H.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)23K18011 Japan
CitationJournal: To Be Published
Title: Structure of Ribosome-inactivating protein from Mirabilis jalapa and stalk-dependent inhibition of E.coli ribosome
Authors: Nishida, N. / Ninomiya, Y. / Yoshida, T. / Tanzawa, T. / Maki, Y. / Yoshida, H. / Tsuge, H. / Habuka, N.
History
DepositionOct 7, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 3, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Antiviral protein MAP
B: Antiviral protein MAP
C: Antiviral protein MAP
D: Antiviral protein MAP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,90017
Polymers114,6514
Non-polymers1,24913
Water14,016778
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7540 Å2
ΔGint-184 kcal/mol
Surface area41650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)214.312, 60.645, 79.254
Angle α, β, γ (deg.)90.000, 109.020, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

#1: Protein
Antiviral protein MAP / MAP-S / Ribosome-inactivating protein / rRNA N-glycosidase


Mass: 28662.699 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mirabilis jalapa (garden four-o'clock) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P21326, rRNA N-glycosylase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 778 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.17 Å3/Da / Density % sol: 43.42 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.2M Ammonium sulfate, 30% w/v Polyethylene glycol 8000

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Data collection

DiffractionMean temperature: 273 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 20, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→43.97 Å / Num. obs: 56406 / % possible obs: 99.87 % / Redundancy: 3.4 % / Biso Wilson estimate: 17.76 Å2 / CC1/2: 0.984 / Rmerge(I) obs: 0.277 / Rpim(I) all: 0.115 / Rrim(I) all: 0.3 / Net I/σ(I): 7.4
Reflection shellResolution: 2.15→2.22 Å / Rmerge(I) obs: 1.052 / Mean I/σ(I) obs: 2 / Num. unique obs: 4549 / CC1/2: 0.529 / Rpim(I) all: 0.436 / Rrim(I) all: 1.141

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Processing

Software
NameVersionClassification
PHENIX1.21.2refinement
XDSdata reduction
XDSdata scaling
PHENIX1.21.2phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→43.97 Å / SU ML: 0.2721 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.9312
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2457 2781 4.93 %
Rwork0.1901 53625 -
obs0.1928 56406 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 19.69 Å2
Refinement stepCycle: LAST / Resolution: 2.1→43.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7883 0 65 778 8726
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00638080
X-RAY DIFFRACTIONf_angle_d0.816310955
X-RAY DIFFRACTIONf_chiral_restr0.04711284
X-RAY DIFFRACTIONf_plane_restr0.00581360
X-RAY DIFFRACTIONf_dihedral_angle_d14.37722940
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.140.28691200.23322676X-RAY DIFFRACTION99.57
2.14-2.180.29471270.23812652X-RAY DIFFRACTION99.68
2.18-2.220.31891370.24112656X-RAY DIFFRACTION99.68
2.22-2.260.2871410.22832673X-RAY DIFFRACTION99.68
2.26-2.310.31531580.22462622X-RAY DIFFRACTION99.78
2.31-2.360.30011480.22232629X-RAY DIFFRACTION99.82
2.37-2.420.31151500.2172693X-RAY DIFFRACTION99.82
2.42-2.490.2481440.2052641X-RAY DIFFRACTION99.86
2.49-2.560.26951480.20232655X-RAY DIFFRACTION99.93
2.56-2.650.29171360.20122702X-RAY DIFFRACTION100
2.65-2.740.26671380.1972662X-RAY DIFFRACTION100
2.74-2.850.25111150.19822698X-RAY DIFFRACTION100
2.85-2.980.24821290.18592678X-RAY DIFFRACTION99.96
2.98-3.140.2261410.18062682X-RAY DIFFRACTION99.96
3.14-3.330.23641570.18182680X-RAY DIFFRACTION100
3.33-3.590.22871590.16622685X-RAY DIFFRACTION100
3.59-3.950.20941340.15172686X-RAY DIFFRACTION99.93
3.95-4.520.1741190.14072713X-RAY DIFFRACTION99.96
4.52-5.70.20761390.1672731X-RAY DIFFRACTION100
5.7-43.970.22631410.22282811X-RAY DIFFRACTION99.83
Refinement TLS params.Method: refined / Origin x: 39.191533007722 Å / Origin y: 17.314506860466 Å / Origin z: -36.051086559798 Å
111213212223313233
T0.099793771301802 Å2-0.0041273754754775 Å2-0.0010232782763588 Å2-0.10246811055759 Å20.0011212742509117 Å2--0.1011240864334 Å2
L0.054302437115213 °2-0.012607366965261 °2-0.0037011595690047 °2-0.063396983088239 °2-0.0095386097555262 °2--0.014675683645116 °2
S0.00027331047863573 Å °0.007534819308633 Å °-0.00029285296448263 Å °-0.0030987927952152 Å °-0.0071328248489259 Å °-0.0031593143708828 Å °0.0016000465629416 Å °0.0040287239179408 Å °-3.391491E-12 Å °
Refinement TLS groupSelection details: all

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