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- PDB-2jjr: V232K, N236D-trichosanthin -

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Basic information

Entry
Database: PDB / ID: 2jjr
TitleV232K, N236D-trichosanthin
ComponentsRIBOSOME-INACTIVATING PROTEIN ALPHA-TRICHOSANTHIN
KeywordsHYDROLASE / ANTIVIRAL PROTEIN / PROTEIN SYNTHESIS INHIBITOR / TCS / TOXIN / PLANT DEFENSE
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
DI(HYDROXYETHYL)ETHER / Ribosome-inactivating protein alpha-trichosanthin
Similarity search - Component
Biological speciesTRICHOSANTHES KIRILOWII (Chinese cucumber)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsToo, P.H. / Ma, M.K. / Mak, A.N. / Tung, C.K. / Zhu, G. / Au, S.W. / Wong, K.B. / Shaw, P.C.
CitationJournal: Nucleic Acids Res. / Year: 2009
Title: The C-Terminal Fragment of the Ribosomal P Protein Complexed to Trichosanthin Reveals the Interaction between the Ribosome-Inactivating Protein and the Ribosome.
Authors: Too, P.H. / Ma, M.K. / Mak, A.N. / Wong, Y.T. / Tung, C.K. / Zhu, G. / Au, S.W. / Wong, K.B. / Shaw, P.C.
History
DepositionApr 21, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 30, 2008Provider: repository / Type: Initial release
Revision 1.1May 7, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 28, 2017Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.4Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)28,37212
Polymers27,1981
Non-polymers1,17411
Water2,954164
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)73.640, 73.640, 143.443
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein RIBOSOME-INACTIVATING PROTEIN ALPHA-TRICHOSANTHIN / TRICHOSANTHIN MUTANT V232K N236D / RRNA N-GLYCOSIDASE / ALPHA-TCS


Mass: 27197.805 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) TRICHOSANTHES KIRILOWII (Chinese cucumber)
Plasmid: PET / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): (DE3)PLYSS / References: UniProt: P09989, rRNA N-glycosylase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-TAM / TRIS(HYDROXYETHYL)AMINOMETHANE


Mass: 163.215 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H17NO3 / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 164 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, VAL 255 TO LYS ENGINEERED RESIDUE IN CHAIN A, ASN 259 TO ASP

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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: 3.74 Å3/Da / Density % sol: 66.84 % / Description: NONE
Crystal growDetails: 2% PEG 8000, 1.0 M LITHIUM SULFATE

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418
DetectorType: RIGAKU IMAGE PLATE / Detector: IMAGE PLATE / Date: Jun 29, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→35.67 Å / Num. obs: 20607 / % possible obs: 99.7 % / Observed criterion σ(I): 3 / Redundancy: 3.7 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 17.8
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.2 / Mean I/σ(I) obs: 4.9 / % possible all: 98.7

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
CCP4data scaling
MOSFLMphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1TCS

1tcs


Resolution: 2.3→63.76 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.924 / SU B: 3.922 / SU ML: 0.101 / Cross valid method: THROUGHOUT / ESU R: 0.191 / ESU R Free: 0.166 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.214 1051 5.1 %RANDOM
Rwork0.184 ---
obs0.186 19527 99.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.54 Å2
Baniso -1Baniso -2Baniso -3
1-1.12 Å20.56 Å20 Å2
2--1.12 Å20 Å2
3----1.68 Å2
Refinement stepCycle: LAST / Resolution: 2.3→63.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1911 0 70 164 2145
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0222002
X-RAY DIFFRACTIONr_bond_other_d0.0010.021841
X-RAY DIFFRACTIONr_angle_refined_deg1.3851.9882704
X-RAY DIFFRACTIONr_angle_other_deg0.8634272
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.195245
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.24324.11885
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.68215331
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.6351513
X-RAY DIFFRACTIONr_chiral_restr0.090.2310
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022167
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02393
X-RAY DIFFRACTIONr_nbd_refined0.1970.2365
X-RAY DIFFRACTIONr_nbd_other0.1880.21813
X-RAY DIFFRACTIONr_nbtor_refined0.1710.2974
X-RAY DIFFRACTIONr_nbtor_other0.0850.21080
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1570.2160
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1320.213
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2070.235
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1280.212
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9631.51586
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.10621986
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.8113894
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.6144.5718
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.237 83
Rwork0.19 1381

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