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- PDB-9tpf: The structure of the orthorhombic crystal form of the type II rib... -

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Basic information

Entry
Database: PDB / ID: 9tpf
TitleThe structure of the orthorhombic 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 / homology1-deoxy-alpha-D-mannopyranose / alpha-L-fucopyranose / alpha-D-mannopyranose
Function and homology information
Biological speciesEranthis hyemalis (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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 18, 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)57,76515
Polymers55,7512
Non-polymers2,01313
Water12,250680
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6170 Å2
ΔGint-71 kcal/mol
Surface area20620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.589, 95.47, 96.339
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP212121

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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)
#2: Protein Lectin


Mass: 28964.096 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Eranthis hyemalis (plant)

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Sugars , 4 types, 7 molecules

#3: 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.: 4 / 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
#4: Sugar ChemComp-MAN / alpha-D-mannopyranose / alpha-D-mannose / D-mannose / mannose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H12O6
IdentifierTypeProgram
DManpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-mannopyranoseCOMMON NAMEGMML 1.0
a-D-ManpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
ManSNFG 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
#9: Sugar ChemComp-AH2 / 1-deoxy-alpha-D-mannopyranose / 1,5-Anhydromannitol / 1-deoxy-alpha-D-mannose / 1-deoxy-D-mannose / 1-deoxy-mannose


Type: D-saccharide / Mass: 164.156 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H12O5

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Non-polymers , 4 types, 686 molecules

#6: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#7: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#8: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 680 / 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: 3.32 Å3/Da / Density % sol: 62.99 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: The crystal was grown at 4 degrees C in PACT condition B12 (0.01 M zinc chloride, 0.1 M MES pH 6, 20 % PEG 6000).

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9282 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 11, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9282 Å / Relative weight: 1
ReflectionResolution: 1.77→67.8 Å / Num. obs: 72825 / % possible obs: 99.7 % / Redundancy: 13.3 % / CC1/2: 0.999 / Rmerge(I) obs: 0.106 / Rrim(I) all: 0.11 / Χ2: 0.96 / Net I/σ(I): 14.8
Reflection shellResolution: 1.77→1.81 Å / Redundancy: 12.5 % / Rmerge(I) obs: 2.552 / Mean I/σ(I) obs: 1 / Num. unique obs: 4058 / CC1/2: 0.629 / Rrim(I) all: 2.661 / Χ2: 0.91 / % possible all: 99.3

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Processing

Software
NameVersionClassification
Servalcat0.4.105refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→47.735 Å / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflection
Rfree0.2333 3452 -
Rwork0.1823 66017 -
obs-69469 99.97 %
Displacement parametersBiso mean: 39.79 Å2
Baniso -1Baniso -2Baniso -3
1-0.974573188 Å20 Å20 Å2
2---16.04594 Å20 Å2
3---15.0713668 Å2
Refinement stepCycle: LAST / Resolution: 1.8→47.735 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3919 0 118 680 4717
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONs_bond_nonh_d0.012141410.0117
X-RAY DIFFRACTIONs_angle_nonh_deg2.004156401.7849
X-RAY DIFFRACTIONs_dihedral_angle_1_deg6.99665065
X-RAY DIFFRACTIONs_dihedral_angle_2_deg4.54351655
X-RAY DIFFRACTIONs_dihedral_angle_3_deg10.744398410
X-RAY DIFFRACTIONs_dihedral_angle_6_deg13.885424610
X-RAY DIFFRACTIONs_chiral_restr0.08716610.1282
X-RAY DIFFRACTIONs_planes0.009359900.02
X-RAY DIFFRACTIONs_nbd0.230853580.2
X-RAY DIFFRACTIONs_nbtor0.224467090.2
X-RAY DIFFRACTIONs_hbond_nbd0.24652720.2
X-RAY DIFFRACTIONs_metal_ion0.114330.2
X-RAY DIFFRACTIONs_symmetry_nbd0.1782820.2
X-RAY DIFFRACTIONs_symmetry_hbond_nbd0.1734160.2
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 (%)
1.8-1.8420.40392030.360644060.83680.8251460999.91
1.842-1.8880.35872480.335542450.86180.8437449399.93
1.888-1.9370.37232250.315341940.87330.8216441999.93
1.937-1.990.3612350.28940510.89890.8026428699.88
1.99-2.0470.32391910.270339740.89110.8703416599.93
2.047-2.110.29071970.251338560.90790.87694053100
2.11-2.1790.28131710.230137610.91670.8517393299.97
2.179-2.2560.23041870.201336340.93440.92793821100
2.256-2.340.26381800.194435060.93420.8716368699.97
2.34-2.4360.26042020.184733420.93610.81093544100
2.436-2.5440.25751870.179132420.93740.84183429100
2.544-2.6680.25661590.173931050.93340.8585326499.97
2.668-2.8110.21521270.172329730.930.90123100100
2.811-2.9810.23221620.168428170.9350.87122979100
2.981-3.1860.22641390.172726180.93740.9052757100
3.186-3.440.23521230.17824670.93990.87512590100
3.44-3.7670.20771120.162223130.94340.89272425100
3.767-4.2080.2039810.132221030.95950.90822184100
4.208-4.8530.14181190.111718290.96980.94761948100
4.853-5.9280.2095930.143615690.95960.92011662100
5.928-8.3190.2402770.185812440.93680.88131321100
8.319-47.7350.1755340.20487680.87510.9244802100

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