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- PDB-1giu: A TRICHOSANTHIN(TCS) MUTANT(E85R) COMPLEX STRUCTURE WITH ADENINE -

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Basic information

Entry
Database: PDB / ID: 1giu
TitleA TRICHOSANTHIN(TCS) MUTANT(E85R) COMPLEX STRUCTURE WITH ADENINE
ComponentsRIBOSOME-INACTIVATING PROTEIN ALPHA-TRICHOSANTHIN
KeywordsHYDROLASE / PROTEIN-SUB COMPLEX / TRICHOSANTHIN / TCS
Function / homology
Function and homology information


regulation of defense response to virus / rRNA N-glycosylase / rRNA N-glycosylase activity / defense response / toxin activity / negative regulation of translation
Similarity search - Function
Ricin (A Subunit), domain 2 / Ricin (A Subunit), domain 2 / Ricin (A subunit); domain 1 / Ricin (A subunit), domain 1 / 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 ...Ricin (A Subunit), domain 2 / Ricin (A Subunit), domain 2 / Ricin (A subunit); domain 1 / Ricin (A subunit), domain 1 / 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 / Few Secondary Structures / Irregular / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENINE / Ribosome-inactivating protein alpha-trichosanthin
Similarity search - Component
Biological speciesTrichosanthes kirilowii (Chinese cucumber)
MethodX-RAY DIFFRACTION / Resolution: 1.8 Å
AuthorsGuo, Q. / Liu, Y. / Dong, Y. / Rao, Z.
CitationJournal: Protein Eng. / Year: 2003
Title: Substrate binding and catalysis in trichosanthin occur in different sites as revealed by the complex structures of several E85 mutants.
Authors: Guo, Q. / Zhou, W. / Too, H.M. / Li, J. / Liu, Y. / Bartlam, M. / Dong, Y. / Wong, K.B. / Shaw, P.C. / Rao, Z.
History
DepositionMar 15, 2001Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 3, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 10, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RIBOSOME-INACTIVATING PROTEIN ALPHA-TRICHOSANTHIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,3302
Polymers27,1951
Non-polymers1351
Water3,243180
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)38.0, 75.3, 78.4
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein RIBOSOME-INACTIVATING PROTEIN ALPHA-TRICHOSANTHIN


Mass: 27194.850 Da / Num. of mol.: 1 / Mutation: E85R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trichosanthes kirilowii (Chinese cucumber)
Production host: Escherichia coli (E. coli) / References: UniProt: P09989, rRNA N-glycosylase
#2: Chemical ChemComp-ADE / ADENINE


Mass: 135.127 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H5N5
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 180 / Source method: isolated from a natural source / Formula: H2O

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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: 2.06 Å3/Da / Density % sol: 40.34 %
Crystal growTemperature: 291 K / Method: evaporation / pH: 5.7
Details: CaCl2, KCl, NaAC-HAC, pH 5.7, EVAPORATION, temperature 291.0K
Crystal grow
*PLUS
Temperature: 291 K / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
140 mg/mlprotein1drop
2100 mM1reservoirpH5.7NaOAc-HOAc
320 %1reservoirKCl
4100 mM1reservoirCaCl2

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Dec 29, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. all: 21505 / Num. obs: 21401 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Biso Wilson estimate: 8.7 Å2 / Rmerge(I) obs: 0.077 / Net I/σ(I): 6.8
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.517 / Num. unique all: 2062 / % possible all: 99.2
Reflection
*PLUS
Lowest resolution: 50 Å
Reflection shell
*PLUS
% possible obs: 99.2 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS1refinement
RefinementResolution: 1.8→50 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber / Details: CNS
RfactorNum. reflection% reflection
Rfree0.247 1001 -
Rwork0.21 --
all0.21 21505 -
obs0.21 20470 95.2 %
Refinement stepCycle: LAST / Resolution: 1.8→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1915 0 10 180 2105
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.019
X-RAY DIFFRACTIONc_angle_deg1.29
Refinement
*PLUS
Lowest resolution: 30 Å / % reflection Rfree: 5 % / Rfactor obs: 0.21 / Rfactor Rwork: 0.21
Solvent computation
*PLUS
Displacement parameters
*PLUS

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