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- PDB-1nli: Complex of [E160A-E189A] trichosanthin and adenine -

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Basic information

Entry
Database: PDB / ID: 1nli
TitleComplex of [E160A-E189A] trichosanthin and adenine
ComponentsRibosome-inactivating protein alpha-trichosanthin
KeywordsHYDROLASE / protein-DNA complex / ribosome-inactivating protein
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 / MOLECULAR REPLACEMENT / Resolution: 1.93 Å
AuthorsShaw, P.C. / Wong, K.B. / Chan, D.S.B. / Williams, R.L.
CitationJournal: Toxicon / Year: 2003
Title: Structural basis for the interaction of [E160A-E189A]-trichosanthin with adenine.
Authors: Shaw, P.C. / Wong, K.B. / Chan, D.S. / Williams, R.L.
History
DepositionJan 7, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 21, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 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 1.4Aug 16, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)27,3172
Polymers27,1821
Non-polymers1351
Water3,675204
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)37.928, 75.299, 78.650
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 Ribosome-inactivating protein alpha-trichosanthin / trichosanthin / rRNA N-glycosidase / Alpha-TCS


Mass: 27181.895 Da / Num. of mol.: 1 / Mutation: E160A, E189A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trichosanthes kirilowii (Chinese cucumber)
Gene: Trichosanthin / Plasmid: pET8C / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 [DE3, pLysS] / 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.: 204 / 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: 2.07 Å3/Da / Density % sol: 40.44 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: Tris-HCl, PEG4000, magnesium chloride, adenine hemisulfate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Crystal grow
*PLUS
Temperature: 16 ℃ / pH: 6
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
185 mM1dropNaCl
220 mMpotassium phosphate1droppH6.0
320 mg/mlprotein1drop
40.1 MTris-HCl1reservoirpH6.5
520 %PEG40001reservoir
60.1 M1reservoirMgCl2
72.7 mMadenine hemisulfate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 3, 2001 / Details: Mirrors
RadiationMonochromator: Ni filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.93→54.391 Å / Num. obs: 16683 / % possible obs: 99.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.7 % / Biso Wilson estimate: 12.008 Å2 / Rmerge(I) obs: 0.056 / Rsym value: 0.056 / Net I/σ(I): 9.2
Reflection shellResolution: 1.93→2.03 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.155 / Mean I/σ(I) obs: 5.4 / Num. unique all: 2290 / Rsym value: 0.132 / % possible all: 99.3
Reflection
*PLUS
Lowest resolution: 54.4 Å / Num. obs: 17397 / Rmerge(I) obs: 0.065
Reflection shell
*PLUS
Lowest resolution: 2.04 Å / % possible obs: 95.9 %

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
TRUNCATEdata reduction
AMoREphasing
REFMACrefinement
CCP4(TRUNCATE)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB Entry 1QD2

1qd2


Resolution: 1.93→54.23 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.901 / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20771 878 5.1 %RANDOM
Rwork0.15758 ---
all0.16011 20467 --
obs0.16011 16473 99.3 %-
Solvent computationShrinkage radii: 0.8 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 10.951 Å2
Baniso -1Baniso -2Baniso -3
1--1.3 Å20 Å20 Å2
2--0.73 Å20 Å2
3---0.58 Å2
Refinement stepCycle: LAST / Resolution: 1.93→54.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1913 0 10 204 2127
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0221956
X-RAY DIFFRACTIONr_bond_other_d0.0020.021794
X-RAY DIFFRACTIONr_angle_refined_deg1.7751.9582657
X-RAY DIFFRACTIONr_angle_other_deg0.92634156
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0555247
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_chiral_restr0.1110.2312
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022179
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02395
X-RAY DIFFRACTIONr_nbd_refined0.2210.2386
X-RAY DIFFRACTIONr_nbd_other0.2540.22062
X-RAY DIFFRACTIONr_nbtor_other0.0910.21153
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1440.2121
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2580.210
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3060.252
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1730.220
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it1.0631.51236
X-RAY DIFFRACTIONr_mcangle_it1.83821992
X-RAY DIFFRACTIONr_scbond_it3.073720
X-RAY DIFFRACTIONr_scangle_it4.8744.5665
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.934→1.984 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.201 53
Rwork0.161 1136
Refinement
*PLUS
Lowest resolution: 54.4 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.208 / Rfactor Rwork: 0.158
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.002
X-RAY DIFFRACTIONr_angle_d1.775

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