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- PDB-8tab: RTA-PD00589 -

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Basic information

Entry
Database: PDB / ID: 8tab
TitleRTA-PD00589
ComponentsRicin A chain
KeywordsTOXIN / HYDROLASE/INHIBITOR / N-glycosidase / inhibitor / 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
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 ...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
Similarity search - Domain/homology
4H,5H-naphtho[1,2-b]thiophene-2-carboxylic acid / Ricin
Similarity search - Component
Biological speciesRicinus communis (castor bean)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.26 Å
AuthorsRudolph, M.J. / Tumer, N.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI072425 United States
CitationJournal: Bioorg.Med.Chem. / Year: 2024
Title: Structure-based design and optimization of a new class of small molecule inhibitors targeting the P-stalk binding pocket of ricin.
Authors: Rudolph, M.J. / Dutta, A. / Tsymbal, A.M. / McLaughlin, J.E. / Chen, Y. / Davis, S.A. / Theodorous, S.A. / Pierce, M. / Algava, B. / Zhang, X. / Szekely, Z. / Roberge, J.Y. / Li, X.P. / Tumer, N.E.
History
DepositionJun 27, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 1, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ricin A chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,8118
Polymers28,9361
Non-polymers8757
Water2,918162
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)169.146, 169.146, 55.913
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322
Components on special symmetry positions
IDModelComponents
11A-442-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Ricin A chain


Mass: 28935.625 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

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Non-polymers , 5 types, 169 molecules

#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-U4T / 4H,5H-naphtho[1,2-b]thiophene-2-carboxylic acid / 4,5-Dihydronaphtho[1,2-b]thiophene-2-carboxylic acid / 4,5-dihydrobenzo[g][1]benzothiole-2-carboxylic acid


Mass: 230.282 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H10O2S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-2PE / NONAETHYLENE GLYCOL


Mass: 414.488 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H38O10 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 162 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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: 3.99 Å3/Da / Density % sol: 69.17 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 200 mM Mg(NO3)2 and 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 10, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.25→50 Å / Num. obs: 22196 / % possible obs: 99.2 % / Redundancy: 10.3 % / Rmerge(I) obs: 0.2 / Net I/σ(I): 4.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2.25-2.297.91.42210300.6140.8720.5151.5180.49792.6
2.29-2.3381.29910510.5590.8470.4711.3870.5197.9
2.33-2.388.11.36210960.580.8570.5061.4590.50399.3
2.38-2.428.51.25110820.7110.9120.4481.3320.51699.6
2.42-2.488.71.34210990.6820.90.4751.4270.52799.7
2.48-2.538.81.13410910.590.8620.41.2050.55499.9
2.53-2.68.80.99710930.770.9330.351.0590.55899.9
2.6-2.678.80.83510980.8190.9490.2940.8870.57399.9
2.67-2.758.40.69911060.8440.9570.2530.7460.62799.8
2.75-2.837.70.53510900.9020.9740.2040.5750.65699.5
2.83-2.9410.50.50511060.9540.9880.1610.5310.68199.9
2.94-3.0511.60.4211200.9750.9940.1270.440.716100
3.05-3.1912.50.3411060.980.9950.0990.3550.804100
3.19-3.3613.40.26811110.9850.9960.0760.2790.93299.8
3.36-3.5713.60.211110.9930.9980.0570.2081.11499.6
3.57-3.8512.80.15511260.9940.9990.0460.1621.27899.6
3.85-4.2310.10.11411200.9940.9990.0390.1211.48598.1
4.23-4.8511.80.09611250.9960.9990.0310.1011.55499.6
4.85-6.112.80.09611830.9950.9990.0290.11.37599.8
6.1-5012.50.07712520.9970.9990.0220.082.09199.6

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.26→48.83 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 22.56 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2187 1120 5.05 %
Rwork0.1857 --
obs0.1874 22183 97.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.26→48.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2041 0 34 162 2237
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.004
X-RAY DIFFRACTIONf_angle_d0.609
X-RAY DIFFRACTIONf_dihedral_angle_d7.528304
X-RAY DIFFRACTIONf_chiral_restr0.041318
X-RAY DIFFRACTIONf_plane_restr0.006380
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.26-2.360.26681160.23332261X-RAY DIFFRACTION86
2.36-2.490.29551280.24852619X-RAY DIFFRACTION99
2.49-2.640.26381380.2282645X-RAY DIFFRACTION100
2.64-2.840.23671450.2162624X-RAY DIFFRACTION100
2.85-3.130.26181460.20232677X-RAY DIFFRACTION100
3.13-3.580.2051390.18852674X-RAY DIFFRACTION100
3.58-4.510.17851430.14672695X-RAY DIFFRACTION99
4.52-100.21650.16312868X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.28080.28941.02872.43770.95166.94370.23160.00850.4363-0.0239-0.1882-0.3051-0.24490.3216-0.060.1971-0.06110.03010.28640.0320.4427-12.484475.2222-12.5624
24.9963-2.9432-2.91065.91242.07984.1797-0.3708-1.08720.36120.56570.3013-0.9727-0.05160.68550.07090.2638-0.0696-0.07840.5142-0.05320.34-3.07972.03924.0345
33.431-0.69831.91610.35730.2243.84950.0328-0.03040.03940.02260.04080.0939-0.19120.1741-0.06360.2252-0.02380.06130.238-0.02250.5088-21.99673.1484-3.088
47.7579-0.7564-1.55793.99822.23147.25090.2361-0.58440.51410.51520.01980.4865-0.18750.3628-0.19640.223-0.05970.04540.299-0.04010.4127-24.878874.24736.4882
53.90150.9281-4.67581.5992-2.0548.8737-0.0789-0.0405-0.2005-0.07030.0550.31340.54330.02230.06580.2393-0.03480.01890.25640.00170.6125-24.482655.2758-6.5854
62.553-0.12230.03180.65940.0160.6016-0.0171-0.0375-0.35660.01170.03510.150.0339-0.0178-0.01570.1955-0.02970.00510.24040.02270.4467-18.38361.9507-10.7051
74.4620.80341.80723.1931.27162.34140.0792-0.4658-0.69930.31890.0112-0.43850.29950.0067-0.16190.2056-0.00020.04330.40480.12390.5849-0.440753.4932-2.305
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 32 )
2X-RAY DIFFRACTION2chain 'A' and (resid 33 through 56 )
3X-RAY DIFFRACTION3chain 'A' and (resid 57 through 97 )
4X-RAY DIFFRACTION4chain 'A' and (resid 98 through 122 )
5X-RAY DIFFRACTION5chain 'A' and (resid 123 through 140 )
6X-RAY DIFFRACTION6chain 'A' and (resid 141 through 219 )
7X-RAY DIFFRACTION7chain 'A' and (resid 220 through 261 )

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