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- PDB-8t9v: RTA-RUNT-59 complex structure -

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Basic information

Entry
Database: PDB / ID: 8t9v
TitleRTA-RUNT-59 complex structure
ComponentsRicin
KeywordsTOXIN / N-glycosidase / inhibitors
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
Biological speciesRicinus communis (castor bean)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.945 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 26, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 1, 2024Provider: repository / Type: Initial release

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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)29,5983
Polymers28,9361
Non-polymers6632
Water1,946108
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)169.078, 169.078, 54.772
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-444-

HOH

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Components

#1: Protein Ricin


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
#2: Chemical ChemComp-ZJT / (9aP)-7-fluoro-4,5-dihydronaphtho[1,2-b]thiophene-2-carboxylic acid


Mass: 248.273 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H9FO2S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-2PE / NONAETHYLENE GLYCOL


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


Mass: 18.015 Da / Num. of mol.: 108 / 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: 3.95 Å3/Da / Density % sol: 68.86 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 200 mM di-Ammonium tartrate 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: Sep 27, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.945→50 Å / Num. obs: 34295 / % possible obs: 100 % / Redundancy: 20 % / Rmerge(I) obs: 0.14 / Net I/σ(I): 4.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
1.95-1.9821.63.66516840.5280.8310.8083.7550.343100
1.98-2.0222.33.22316810.6420.8840.7013.30.349100
2.02-2.0622.92.68316770.770.9330.5742.7450.354100
2.06-2.123.42.2316810.8080.9460.4722.2810.36100
2.1-2.15241.87216900.8710.9650.3911.9130.359100
2.15-2.224.11.53417010.930.9820.3191.5680.371100
2.2-2.2523.91.21716610.960.990.2551.2440.385100
2.25-2.3123.80.99717000.9720.9930.2091.0190.396100
2.31-2.3823.10.79216910.9810.9950.1690.8110.408100
2.38-2.4620.60.64116840.9820.9950.1450.6570.42100
2.46-2.5424.90.56817110.9840.9960.1160.580.446100
2.54-2.65270.43617010.9890.9970.0860.4450.463100
2.65-2.7727.20.33617090.9930.9980.0660.3430.514100
2.77-2.9127.40.24117120.9970.9990.0480.2460.6100
2.91-3.127.90.1917100.9970.9990.0370.1930.799.9
3.1-3.33280.13417280.9970.9990.0270.1370.898100
3.33-3.6725.70.09817440.99810.020.11.21599.9
3.67-4.230.20.07817490.99910.0160.081.4999.8
4.2-5.2927.60.06117710.99910.0130.0621.639100
5.29-5028.70.0471910110.0090.0481.56499.8

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.945→48.809 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.45 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2059 1667 4.87 %
Rwork0.1765 --
obs0.178 34257 99.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.945→48.809 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2041 0 24 108 2173
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0152121
X-RAY DIFFRACTIONf_angle_d1.1952884
X-RAY DIFFRACTIONf_dihedral_angle_d4.351731
X-RAY DIFFRACTIONf_chiral_restr0.07318
X-RAY DIFFRACTIONf_plane_restr0.008380
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9452-2.00250.43181310.39462610X-RAY DIFFRACTION98
2.0025-2.06710.38581140.34232699X-RAY DIFFRACTION100
2.0671-2.1410.31771340.28582681X-RAY DIFFRACTION100
2.141-2.22670.26981380.23872669X-RAY DIFFRACTION100
2.2267-2.32810.251280.20492683X-RAY DIFFRACTION100
2.3281-2.45080.22561350.19532686X-RAY DIFFRACTION100
2.4508-2.60430.22051520.19142703X-RAY DIFFRACTION100
2.6043-2.80540.23361350.18952699X-RAY DIFFRACTION100
2.8054-3.08770.23611320.19162722X-RAY DIFFRACTION100
3.0877-3.53440.20881550.18282727X-RAY DIFFRACTION100
3.5344-4.45240.1671460.13832786X-RAY DIFFRACTION100
4.4524-48.8090.16591670.14292925X-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)
10.362-0.56880.02322.5973-0.20970.02180.3284-0.02990.8208-0.06840.0661-0.2344-0.82950.2532-0.35270.4739-0.09590.07460.5829-0.03330.5715-16.616878.308-10.8589
24.0586-0.11730.99563.39350.51418.19640.31220.10240.4588-0.1001-0.1792-0.3932-0.58180.8933-0.20110.3251-0.05540.06370.59180.02170.5783-8.84772.5385-13.4738
37.2093-3.6358-2.87554.88892.4044.3056-0.1732-1.6690.69020.55820.3826-0.8047-0.18540.9158-0.07060.3796-0.163-0.07190.8746-0.10390.5728-3.11471.99754.0661
44.3208-0.03851.5720.67120.31694.11920.217-0.09830.18490.0952-0.00680.1049-0.21860.3607-0.14680.3166-0.05920.04750.3768-0.03090.5393-22.003773.104-2.9387
54.97590.1386-1.98066.22550.76245.14910.4074-1.04190.56520.6724-0.14480.1508-0.40820.4613-0.27370.4168-0.12160.05820.5502-0.120.5124-24.930974.16856.6318
63.370.0589-1.34632.3828-0.80213.149-0.00930.1084-0.4077-0.109-0.03440.41230.30390.03410.07370.2752-0.0614-0.01030.3884-0.02970.5918-26.283461.4378-9.3531
76.0586-1.1064-1.18111.4794-0.3682.35520.13720.0845-0.0084-0.037-0.01510.2538-0.0424-0.2476-0.04620.2755-0.01710.020.34260.01720.4764-28.454764.2093-7.7452
83.42311.1546-0.06432.7270.64761.67390.113-0.1815-0.84080.1183-0.0982-0.03170.20460.3329-0.00160.235-0.00450.00590.49480.05240.5698-8.2657.6971-8.6244
93.92110.75432.69531.27490.80522.58160.2358-0.6298-1.19980.6423-0.1653-0.59450.690.2155-0.1170.42390.0174-0.01410.67690.11080.7234-2.169553.6347-4.0883
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 17 )
2X-RAY DIFFRACTION2chain 'A' and (resid 18 through 32 )
3X-RAY DIFFRACTION3chain 'A' and (resid 33 through 56 )
4X-RAY DIFFRACTION4chain 'A' and (resid 57 through 97 )
5X-RAY DIFFRACTION5chain 'A' and (resid 98 through 122 )
6X-RAY DIFFRACTION6chain 'A' and (resid 123 through 154 )
7X-RAY DIFFRACTION7chain 'A' and (resid 155 through 174 )
8X-RAY DIFFRACTION8chain 'A' and (resid 175 through 229 )
9X-RAY DIFFRACTION9chain 'A' and (resid 230 through 261 )

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