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- PDB-1qd2: CRYSTAL STRUCTURE OF THE COMPLEX OF TRICHOSANTHIN WITH ADENINE, O... -

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Basic information

Entry
Database: PDB / ID: 1qd2
TitleCRYSTAL STRUCTURE OF THE COMPLEX OF TRICHOSANTHIN WITH ADENINE, OBTAINED FROM TRICHOSANTHIN COMPLEXED WITH THE DINUCLEOTIDE APG
ComponentsTRICHOSANTHIN
KeywordsHYDROLASE / ENZYME-PRODUCT COMPLEX OBTAINED FROM ENZYME-SUBSTRATE ANALOG COMPLEX
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: 1.86 Å
AuthorsGu, Y.J. / Xia, Z.X.
CitationJournal: Proteins / Year: 2000
Title: Crystal structures of the complexes of trichosanthin with four substrate analogs and catalytic mechanism of RNA N-glycosidase.
Authors: Gu, Y.J. / Xia, Z.X.
History
DepositionJul 9, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 24, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TRICHOSANTHIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,3022
Polymers27,1671
Non-polymers1351
Water3,405189
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)38.41, 76.72, 79.45
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Cell settingorthorhombic
Space group name H-MP212121

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Components

#1: Protein TRICHOSANTHIN / E.C.3.2.2.22 / RIBOSOME-INACTIVATING PROTEIN ALPHA-TRICHOSANTHIN / RRNA N-GLYCOSIDASE / ALPHA-TCS


Mass: 27166.770 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Trichosanthes kirilowii (Chinese cucumber)
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.: 189 / 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: 2.15 Å3/Da / Density % sol: 42.89 %
Crystal growTemperature: 281 K / Method: vapor diffusion, hanging drop / pH: 5
Details: HANGING DROP, CITRATE BUFFER, POTASSIUM CHLORIDE, DINUCLEOTIDE APG. NATIVE CRYSTALS SOAKED IN SOLUTION CONTAINING DINUCLEOTIDE APG, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 281K
Crystal grow
*PLUS
Temperature: 20 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
120 mg/mlprotein1drop
20.004 Mcitrate1drop
31-2 mg/mlcorresponding substrates1drop
47 %1dropKCl
514 %1reservoirKCl
60.008 Msodium citrate1reservoir

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SEALED TUBE / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 15, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.86→10 Å / Num. all: 20045 / Num. obs: 20045 / % possible obs: 98.8 % / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 11.25 Å2 / Rmerge(I) obs: 0.078 / Net I/σ(I): 20
Reflection shellResolution: 1.86→1.9 Å / Redundancy: 3 % / Rmerge(I) obs: 0.343 / % possible all: 90.3
Reflection
*PLUS
Reflection shell
*PLUS
% possible obs: 90.3 %

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Processing

Software
NameVersionClassification
X-PLORmodel building
X-PLOR3.1refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementResolution: 1.86→10 Å / σ(F): 2 / Stereochemistry target values: X-PLOR DICTIONARY
RfactorNum. reflection% reflectionSelection details
Rfree0.221 1812 10 %RANDOM
Rwork0.163 ---
obs0.163 18512 92.4 %-
all-20045 --
Refinement stepCycle: LAST / Resolution: 1.86→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1914 0 10 189 2113
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.014
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.266
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 10 Å / σ(F): 2 / % reflection Rfree: 10 %
Solvent computation
*PLUS
Displacement parameters
*PLUS

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