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- PDB-6urx: Crystal structure of ricin A chain in complex with inhibitor 5-ph... -

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Basic information

Entry
Database: PDB / ID: 6urx
TitleCrystal structure of ricin A chain in complex with inhibitor 5-phenyl-2-thiophenecarboxylic acid
ComponentsRicin
KeywordsHydrolase/Hydrolase Inhibitor / Ricin A chain / RTA / Hydrolase / Toxin / Inhibitor / Hydrolase-Hydrolase Inhibitor complex
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
5-phenylthiophene-2-carboxylic acid / Ricin
Similarity search - Component
Biological speciesRicinus communis (castor bean)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.99 Å
AuthorsHarijan, R.K. / Li, X.P. / Bonanno, J.B. / Almo, S.C. / Tumer, N.E. / Schramm, V.L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: Acs Infect Dis. / Year: 2020
Title: Small Molecule Inhibitors Targeting the Interaction of Ricin Toxin A Subunit with Ribosomes.
Authors: Li, X.P. / Harijan, R.K. / Kahn, J.N. / Schramm, V.L. / Tumer, N.E.
History
DepositionOct 24, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 17, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 22, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ricin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,28118
Polymers30,0681
Non-polymers1,21317
Water3,549197
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)168.355, 168.355, 54.834
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number182
Space group name H-MP6322

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Components

#1: Protein Ricin


Mass: 30067.953 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ricinus communis (castor bean) / Production host: Escherichia coli (E. coli) / References: UniProt: P02879, rRNA N-glycosylase
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-JMG / 5-phenylthiophene-2-carboxylic acid


Mass: 204.245 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H8O2S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 197 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 3.7 Å3/Da / Density % sol: 67.03 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / Details: 200 mM Ammonium Iodide, 20% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.97931 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Mar 7, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97931 Å / Relative weight: 1
ReflectionResolution: 1.99→145.8 Å / Num. obs: 31903 / % possible obs: 100 % / Redundancy: 24.3 % / CC1/2: 0.99 / Rmerge(I) obs: 0.2 / Rpim(I) all: 0.04 / Net I/σ(I): 17.6
Reflection shellResolution: 1.99→2.04 Å / Rmerge(I) obs: 2.22 / Mean I/σ(I) obs: 2 / Num. unique obs: 2190 / CC1/2: 0.81 / Rpim(I) all: 0.46

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
PDB_EXTRACT3.25data extraction
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1RTC

1rtc


Resolution: 1.99→145.8 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.951 / SU B: 4.125 / SU ML: 0.105 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.125 / ESU R Free: 0.123
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.218 1566 4.9 %RANDOM
Rwork0.1843 ---
obs0.1859 30309 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 115.03 Å2 / Biso mean: 34.023 Å2 / Biso min: 22.4 Å2
Baniso -1Baniso -2Baniso -3
1--1.84 Å2-0.92 Å20 Å2
2---1.84 Å20 Å2
3---5.96 Å2
Refinement stepCycle: final / Resolution: 1.99→145.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2060 0 78 198 2336
Biso mean--47.02 44.27 -
Num. residues----261
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0192168
X-RAY DIFFRACTIONr_bond_other_d0.0020.021998
X-RAY DIFFRACTIONr_angle_refined_deg1.4281.9682918
X-RAY DIFFRACTIONr_angle_other_deg0.99534592
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6215260
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.84523.019106
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.79215328
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.621521
X-RAY DIFFRACTIONr_chiral_restr0.0910.2321
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212402
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02472
LS refinement shellResolution: 1.99→2.042 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.316 133 -
Rwork0.309 2174 -
all-2307 -
obs--100 %

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