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- PDB-3ej5: complex of Ricin A chain and pyrimidine-based inhibitor -

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Basic information

Entry
Database: PDB / ID: 3ej5
Titlecomplex of Ricin A chain and pyrimidine-based inhibitor
ComponentsRicin A chain
KeywordsHYDROLASE / protein inhibitor complex / Glycoprotein / Lectin / Nucleotide-binding / Plant defense / Protein synthesis inhibitor / Toxin
Function / homology
Function and homology information


rRNA N-glycosylase / rRNA N-glycosylase activity / AMP binding / defense response / toxin activity / carbohydrate binding / killing of cells of another organism / 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. / Ricin-type beta-trefoil lectin domain / Ribosome-inactivating protein type 1/2 / Ribosome-inactivating protein / Ribosome-inactivating protein, subdomain 1 ...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. / Ricin-type beta-trefoil lectin domain / 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 / Ricin-type beta-trefoil / Lectin domain of ricin B chain profile. / Ricin B, lectin domain / Ricin B-like lectins / Few Secondary Structures / Irregular / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesRicinus communis (castor bean)
MethodX-RAY DIFFRACTION / Resolution: 2.5 Å
AuthorsBai, Y. / Monzingo, A.F. / Robertus, J.D.
CitationJournal: Arch.Biochem.Biophys. / Year: 2009
Title: The X-ray structure of ricin A chain with a novel inhibitor
Authors: Bai, Y. / Monzingo, A.F. / Robertus, J.D.
History
DepositionSep 17, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 7, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
X: Ricin A chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,0522
Polymers28,7621
Non-polymers2891
Water36020
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.642, 68.006, 49.675
Angle α, β, γ (deg.)90.000, 112.970, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Ricin A chain / rRNA N- glycosidase


Mass: 28762.414 Da / Num. of mol.: 1 / Fragment: sequence database residues 40-296
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ricinus communis (castor bean) / Plasmid: PUC18 / Production host: Escherichia coli (E. coli) / Strain (production host): JM101 / References: UniProt: P02879, rRNA N-glycosylase
#2: Chemical ChemComp-EJ5 / 4-[3-(2-amino-4-hydroxy-6-oxo-1,6-dihydropyrimidin-5-yl)propyl]benzoic acid


Mass: 289.287 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H15N3O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 20 / 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: 2.31 Å3/Da / Density % sol: 46.65 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.9
Details: tris-HCl, BME, EDTA, PEG 8000, pH 8.9, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Mar 28, 2008 / Details: varimax
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→30 Å / Num. obs: 9083 / % possible obs: 99.8 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.044 / Χ2: 0.998
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.113 / Num. unique all: 893 / Χ2: 0.706 / % possible all: 99.8

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.006data extraction
MAR345dtbdata collection
HKL-2000data reduction
MOLREPphasing
RefinementStarting model: PDB entry 1RTC

1rtc


Resolution: 2.5→25.7 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.896 / WRfactor Rfree: 0.244 / WRfactor Rwork: 0.188 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.832 / SU B: 19.935 / SU ML: 0.214 / SU R Cruickshank DPI: 1.591 / SU Rfree: 0.335 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.561 / ESU R Free: 0.337 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.266 467 5.2 %RANDOM
Rwork0.194 ---
obs0.198 8936 98.18 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 65.14 Å2 / Biso mean: 25.539 Å2 / Biso min: 5.77 Å2
Baniso -1Baniso -2Baniso -3
1--1.62 Å20 Å2-1.09 Å2
2--0.33 Å20 Å2
3---0.44 Å2
Refinement stepCycle: LAST / Resolution: 2.5→25.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2024 0 21 20 2065
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0222089
X-RAY DIFFRACTIONr_bond_other_d0.0010.021391
X-RAY DIFFRACTIONr_angle_refined_deg1.2371.9592844
X-RAY DIFFRACTIONr_angle_other_deg0.8823.0013348
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2845256
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.86523.301103
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.08415324
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.5021519
X-RAY DIFFRACTIONr_chiral_restr0.0750.2317
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.022363
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02450
X-RAY DIFFRACTIONr_nbd_refined0.2110.2452
X-RAY DIFFRACTIONr_nbd_other0.1950.21473
X-RAY DIFFRACTIONr_nbtor_refined0.1820.21063
X-RAY DIFFRACTIONr_nbtor_other0.0820.21109
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1560.252
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2330.23
X-RAY DIFFRACTIONr_symmetry_vdw_other0.190.221
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1790.24
X-RAY DIFFRACTIONr_mcbond_it1.37331381
X-RAY DIFFRACTIONr_mcbond_other0.253518
X-RAY DIFFRACTIONr_mcangle_it2.1952069
X-RAY DIFFRACTIONr_scbond_it3.6347898
X-RAY DIFFRACTIONr_scangle_it5.06611775
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.416 33 -
Rwork0.248 586 -
all-619 -
obs--94.5 %
Refinement TLS params.Method: refined / Origin x: -2.831 Å / Origin y: 0.6917 Å / Origin z: 8.0857 Å
111213212223313233
T-0.035 Å2-0.0322 Å20.0135 Å2--0.029 Å2-0.014 Å2---0.0391 Å2
L2.0249 °2-0.8068 °20.3285 °2-1.6659 °2-0.1689 °2--1.2561 °2
S-0.0313 Å °0.0118 Å °0.0725 Å °0.0997 Å °0.0112 Å °-0.021 Å °0.0044 Å °0.1251 Å °0.0201 Å °

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