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- PDB-9tpe: The structure of the monoclinic crystal form of the type II ribos... -

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Basic information

Entry
Database: PDB / ID: 9tpe
TitleThe structure of the monoclinic crystal form of the type II ribosome inactivating protein from Winter Aconite Eranthis hyemalis.
Components
  • Lectin
  • N-glycosidase
KeywordsTOXIN / Ribosome inactivating protein N-glycosidase
Function / homologyalpha-L-fucopyranose
Function and homology information
Biological speciesEranthis hyemalis (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsCooper, J.B. / Palmer, R.A.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: The Structure of the Type II Ribosome Inactivating Protein from Winter Aconite Eranthis hyemalis.
Authors: McConnell, M.-T. / Talbert, R.C. / Lee, J.C. / Lisgarten, D.R. / Lisgarten, J. / Bertolo, E. / Harvey, S.C. / Levy, C.W. / Lowe, E.D. / Cooper, J.B. / Naylor, C. / Quiroz, R. / Borges, R. / ...Authors: McConnell, M.-T. / Talbert, R.C. / Lee, J.C. / Lisgarten, D.R. / Lisgarten, J. / Bertolo, E. / Harvey, S.C. / Levy, C.W. / Lowe, E.D. / Cooper, J.B. / Naylor, C. / Quiroz, R. / Borges, R. / Prince, S.M. / Palmer, R.A.
History
DepositionDec 17, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 21, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: N-glycosidase
B: Lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,14810
Polymers55,6802
Non-polymers1,4688
Water14,538807
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5630 Å2
ΔGint12 kcal/mol
Surface area20170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.738, 94.215, 70.876
Angle α, β, γ (deg.)90, 96.44, 90
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein N-glycosidase


Mass: 26787.229 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Eranthis hyemalis (plant) / Plasmid details: Tubers
#2: Protein Lectin


Mass: 28893.018 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Eranthis hyemalis (plant)

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Sugars , 3 types, 4 molecules

#3: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#4: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#5: Sugar ChemComp-FUC / alpha-L-fucopyranose / alpha-L-fucose / 6-deoxy-alpha-L-galactopyranose / L-fucose / fucose


Type: L-saccharide, alpha linking / Mass: 164.156 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H12O5
IdentifierTypeProgram
LFucpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-L-fucopyranoseCOMMON NAMEGMML 1.0
a-L-FucpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
FucSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 3 types, 811 molecules

#6: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#7: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 807 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
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: 2.78 Å3/Da / Density % sol: 55.83 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: The protein was concentrated to 4 mg/ml and a crystal was obtained after 24 weeks at room temperature in condition D10 of the PACT Premier screen (0.2 M magnesium chloride, 0.1 M Tris pH 8, ...Details: The protein was concentrated to 4 mg/ml and a crystal was obtained after 24 weeks at room temperature in condition D10 of the PACT Premier screen (0.2 M magnesium chloride, 0.1 M Tris pH 8, 20 % PEG 6000). The crystal was cryoprotected with a 1:4 ratio of PEG 400 to well solution.
Temp details: Room temperature

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 6, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.5→41.17 Å / Num. obs: 93826 / % possible obs: 99.6 % / Redundancy: 3.3 % / CC1/2: 0.995 / Rmerge(I) obs: 0.063 / Rrim(I) all: 0.075 / Χ2: 1.03 / Net I/σ(I): 13.5
Reflection shellResolution: 1.5→1.53 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.141 / Mean I/σ(I) obs: 5.6 / Num. unique obs: 4509 / CC1/2: 0.956 / Rrim(I) all: 0.179 / Χ2: 0.95 / % possible all: 96.3

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Processing

Software
NameVersionClassification
Servalcat0.4.105refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→29.711 Å / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflection
Rfree0.2065 4810 -
Rwork0.1608 91555 -
obs-96365 98.96 %
Displacement parametersBiso mean: 18.06 Å2
Baniso -1Baniso -2Baniso -3
1-0.950830557 Å20 Å2-1.28292229 Å2
2--5.03046504 Å20 Å2
3----5.98129559 Å2
Refinement stepCycle: LAST / Resolution: 1.5→29.711 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3919 0 94 807 4820
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONs_bond_nonh_d0.013241950.0117
X-RAY DIFFRACTIONs_angle_nonh_deg2.022257381.7839
X-RAY DIFFRACTIONs_dihedral_angle_1_deg6.64515345
X-RAY DIFFRACTIONs_dihedral_angle_2_deg3.54611655
X-RAY DIFFRACTIONs_dihedral_angle_3_deg9.5464101910
X-RAY DIFFRACTIONs_dihedral_angle_6_deg14.545225010
X-RAY DIFFRACTIONs_chiral_restr0.0956740.1285
X-RAY DIFFRACTIONs_planes0.010261180.02
X-RAY DIFFRACTIONs_nbd0.24158060.2
X-RAY DIFFRACTIONs_nbtor0.225968890.2
X-RAY DIFFRACTIONs_hbond_nbd0.26184440.2
X-RAY DIFFRACTIONs_metal_ion0.059710.2
X-RAY DIFFRACTIONs_symmetry_nbd0.18641280.2
X-RAY DIFFRACTIONs_symmetry_hbond_nbd0.2369440.2
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkCor.coef. Fo:FcCor.coef. Fo:Fc freeNum. reflection obs% reflection obs (%)
1.5-1.5320.43132990.410455940.81670.7346589398.69
1.532-1.5670.39492890.360155350.85660.7636582498.66
1.567-1.6030.3612970.300553290.89440.7921562698.24
1.603-1.6430.2822650.245152170.91630.8864548298.28
1.643-1.6850.32112810.223551130.91920.8493539498.45
1.685-1.7310.22592630.198149440.93230.8936520798.26
1.731-1.7810.24482380.191148190.92970.8822505797.83
1.781-1.8360.23392660.180446400.93150.8532490698.04
1.836-1.8960.25642640.17145260.93430.8379479098.22
1.896-1.9620.22652150.164344620.93780.8735467798.57
1.962-2.0360.21412250.152942690.95110.8938449499.18
2.036-2.1190.16892000.146641580.96240.9342435899.48
2.119-2.2120.19622200.143840000.96810.9273422099.83
2.212-2.320.16392170.136737780.97030.9352399599.97
2.32-2.4440.17871770.123436640.96590.9123384199.95
2.444-2.5910.14971860.111734490.96950.9475363599.92
2.591-2.7690.1491670.113432480.96270.926341599.91
2.769-2.9890.16911690.114629660.96210.9191313599.9
2.989-3.2710.13711330.116128020.96040.9446293599.76
3.271-3.6510.16461350.116125140.96170.9152264999.7
3.651-4.2050.14941020.114122620.96650.9483236499.83
4.205-5.1250.2219960.172918950.95870.9135199199.75
5.125-7.1420.2825680.25714880.92410.8814155699.74
7.142-29.7110.3552380.27048830.87250.855792198.71

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