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- PDB-1tcs: CRYSTAL STRUCTURE OF TRICHOSANTHIN-NADPH COMPLEX AT 1.7 ANGSTROMS... -

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Basic information

Entry
Database: PDB / ID: 1tcs
TitleCRYSTAL STRUCTURE OF TRICHOSANTHIN-NADPH COMPLEX AT 1.7 ANGSTROMS RESOLUTION REVEALS ACTIVE-SITE ARCHITECTURE
ComponentsTRICHOSANTHIN
KeywordsPROTEIN SYNTHESIS INHIBITOR / TOXIN
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
Chem-NDP / Ribosome-inactivating protein alpha-trichosanthin
Similarity search - Component
Biological speciesTrichosanthes kirilowii (Chinese cucumber)
MethodX-RAY DIFFRACTION / Resolution: 1.7 Å
AuthorsXiong, J.-P. / Xia, Z.-X. / Wang, Y.
Citation
Journal: Nat.Struct.Biol. / Year: 1994
Title: Crystal structure of trichosanthin-NADPH complex at 1.7 A resolution reveals active-site architecture.
Authors: Xiong, J.P. / Xia, Z.X. / Wang, Y.
#1: Journal: Chin.J.Chem. / Year: 1993
Title: The Three-Dimensional Structure of Trichosanthin Refined at 2.7 Angstroms Resolution
Authors: Xia, Z.-X. / Zhang, L. / Zhang, Z.-M.
#2: Journal: Chin.J.Chem. / Year: 1991
Title: The Revision of Three-Dimensional Structure of Trichosanthin at 3 Angstroms Resolution
Authors: Xia, Z.-X. / Zhang, Z.-M. / Zhang, L.
History
DepositionDec 27, 1994Processing site: BNL
Revision 1.0Jul 10, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.4Feb 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)27,9122
Polymers27,1671
Non-polymers7451
Water2,612145
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)38.390, 76.810, 79.930
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein TRICHOSANTHIN


Mass: 27166.770 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trichosanthes kirilowii (Chinese cucumber)
References: UniProt: P09989, rRNA N-glycosylase
#2: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 145 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.17 Å3/Da / Density % sol: 43.27 %
Crystal
*PLUS
Density % sol: 39.7 %
Crystal grow
*PLUS
Method: unknown
Components of the solutions
*PLUS
Conc.: 5 mM / Common name: NADPH

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Data collection

ReflectionResolution: 1.7→8 Å / Num. obs: 22244 / % possible obs: 86.5 % / Observed criterion σ(I): 3
Reflection
*PLUS
Num. measured all: 79350 / Rmerge(I) obs: 0.0825

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Processing

SoftwareName: PROFFT / Classification: refinement
RefinementRfactor obs: 0.174 / Highest resolution: 1.7 Å
Refinement stepCycle: LAST / Highest resolution: 1.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1914 0 48 145 2107
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0130.02
X-RAY DIFFRACTIONp_angle_d0.0360.03
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0570.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.4131
X-RAY DIFFRACTIONp_mcangle_it2.1281.5
X-RAY DIFFRACTIONp_scbond_it2.7921.5
X-RAY DIFFRACTIONp_scangle_it3.9312
X-RAY DIFFRACTIONp_plane_restr0.020.02
X-RAY DIFFRACTIONp_chiral_restr0.2590.15
X-RAY DIFFRACTIONp_singtor_nbd0.190.5
X-RAY DIFFRACTIONp_multtor_nbd0.2330.5
X-RAY DIFFRACTIONp_xhyhbond_nbd0.2220.5
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor5.83
X-RAY DIFFRACTIONp_staggered_tor19.115
X-RAY DIFFRACTIONp_orthonormal_tor3420
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Refinement
*PLUS
Lowest resolution: 8 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS

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