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Basic information

Entry
Database: PDB / ID: 8cx8
TitleStx2A1-BTB13086
ComponentsrRNA N-glycosylase
KeywordsTOXIN
Function / homology
Function and homology information


rRNA N-glycosylase / rRNA N-glycosylase activity / toxin activity / negative regulation of translation
Similarity search - Function
Shiga-like toxin, subunit A / Ribosome-inactivating protein conserved site / Shiga/ricin ribosomal inactivating toxins active site signature. / Ribosome-inactivating protein / Ribosome-inactivating protein, subdomain 1 / Ribosome-inactivating protein, subdomain 2 / Ribosome-inactivating protein superfamily / Ribosome inactivating protein
Similarity search - Domain/homology
: / rRNA N-glycosylase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.905 Å
AuthorsRudolph, M.J. / Li, X.P.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)1R01AI141635-01A1 United States
CitationJournal: Acs Infect Dis. / Year: 2024
Title: Fragment Screening to Identify Inhibitors Targeting Ribosome Binding of Shiga Toxin 2.
Authors: Rudolph, M.J. / Tsymbal, A.M. / Dutta, A. / Davis, S.A. / Algava, B. / Roberge, J.Y. / Tumer, N.E. / Li, X.P.
History
DepositionMay 20, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 6, 2024Provider: repository / Type: Initial release
Revision 1.1Sep 18, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 16, 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: rRNA N-glycosylase
B: rRNA N-glycosylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,77022
Polymers56,1752
Non-polymers1,59520
Water4,035224
1
A: rRNA N-glycosylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,06012
Polymers28,0881
Non-polymers97311
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: rRNA N-glycosylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,71010
Polymers28,0881
Non-polymers6229
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)71.633, 78.622, 87.337
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 1 through 21 or resid 23...
21(chain B and (resid 1 through 21 or resid 23...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ARGARGARGARG(chain A and (resid 1 through 21 or resid 23...AA1 - 212 - 22
12GLUGLUTHRTHR(chain A and (resid 1 through 21 or resid 23...AA23 - 3624 - 37
13VALVALPHEPHE(chain A and (resid 1 through 21 or resid 23...AA38 - 6439 - 65
14HISHISILEILE(chain A and (resid 1 through 21 or resid 23...AA66 - 9867 - 99
15VALVALGLNGLN(chain A and (resid 1 through 21 or resid 23...AA100 - 175101 - 176
16GLUGLUGLYGLY(chain A and (resid 1 through 21 or resid 23...AA177 - 214178 - 215
17VALVALILEILE(chain A and (resid 1 through 21 or resid 23...AA218 - 223219 - 224
18PHEPHECYSCYS(chain A and (resid 1 through 21 or resid 23...AA225 - 241226 - 242
21ARGARGARGARG(chain B and (resid 1 through 21 or resid 23...BB1 - 212 - 22
22GLUGLUTHRTHR(chain B and (resid 1 through 21 or resid 23...BB23 - 3624 - 37
23VALVALVALVAL(chain B and (resid 1 through 21 or resid 23...BB38 - 5939 - 60
24ALAALAPHEPHE(chain B and (resid 1 through 21 or resid 23...BB62 - 6463 - 65
25METMETMETMET(chain B and (resid 1 through 21 or resid 23...BB01
26VALVALGLNGLN(chain B and (resid 1 through 21 or resid 23...BB100 - 175101 - 176
27GLUGLUILEILE(chain B and (resid 1 through 21 or resid 23...BB177 - 223178 - 224
28PHEPHECYSCYS(chain B and (resid 1 through 21 or resid 23...BB225 - 241226 - 242

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein rRNA N-glycosylase


Mass: 28087.582 Da / Num. of mol.: 2
Fragment: Ribosomal inactivating protein catalytic subunit, residues 23-272
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: UniProt: Q5WPX7, rRNA N-glycosylase

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Non-polymers , 5 types, 244 molecules

#2: Chemical ChemComp-P1U / 5-(4-chlorophenyl)furan-2-carboxylic acid


Mass: 222.624 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H7ClO3
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Cl
#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 224 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
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: 2.19 Å3/Da / Density % sol: 43.94 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 100 mM MES pH 6.5 and magnesium sulfate 1.6 M

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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: Feb 14, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 38250 / % possible obs: 98.6 % / Redundancy: 5.1 % / Rmerge(I) obs: 0.122 / Rpim(I) all: 0.06 / Rrim(I) all: 0.136 / Χ2: 1.236 / Net I/σ(I): 6.4 / Num. measured all: 193882
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.9-1.934.21.25118440.2860.6761.4290.44296.6
1.93-1.974.81.22518590.5390.6121.3740.44298.8
1.97-2.014.81.03918890.7390.5151.1640.48398.2
2.01-2.0550.8419020.8140.4070.9360.51997.9
2.05-2.0950.73718570.8370.3560.8210.55598.4
2.09-2.144.90.618920.8390.2960.6720.60798.5
2.14-2.1950.50818900.9230.2490.5680.66698.6
2.19-2.2550.42218920.9530.2070.4720.73898.6
2.25-2.3250.35218820.9650.1720.3930.77598.7
2.32-2.3950.31219140.9570.1530.3490.90698.7
2.39-2.484.90.26519000.9690.1320.2970.93799.2
2.48-2.584.80.22819230.9740.1150.2561.12299.3
2.58-2.74.40.18618610.9680.0970.2111.35997.2
2.7-2.845.30.16719320.9850.080.1861.44199
2.84-3.025.90.13619280.990.0620.151.799.8
3.02-3.255.80.11119510.9920.0520.1232.01999.5
3.25-3.585.50.08719370.9920.0420.0972.23799.4
3.58-4.095.20.06719540.9940.0340.0762.41698.8
4.09-5.164.70.05519400.9960.0280.0622.42796.9
5.16-505.90.04721030.9970.0210.0521.90699.3

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
SCALEPACKdata scaling
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6X6H

6x6h


Resolution: 1.905→45.279 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 23.76 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2052 1950 5.11 %
Rwork0.1775 36216 -
obs0.1789 38166 97.16 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 118.35 Å2 / Biso mean: 39.5124 Å2 / Biso min: 17.21 Å2
Refinement stepCycle: final / Resolution: 1.905→45.279 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3747 0 83 224 4054
Biso mean--64.3 45.63 -
Num. residues----477
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063922
X-RAY DIFFRACTIONf_angle_d0.7475336
X-RAY DIFFRACTIONf_chiral_restr0.052623
X-RAY DIFFRACTIONf_plane_restr0.005678
X-RAY DIFFRACTIONf_dihedral_angle_d12.222308
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2142X-RAY DIFFRACTION5.404TORSIONAL
12B2142X-RAY DIFFRACTION5.404TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.905-1.95220.32911160.2821204278
1.9522-2.0050.261340.2399255998
2.005-2.0640.28281310.2122260498
2.064-2.13060.24271280.1985260698
2.1306-2.20680.221230.1894258198
2.2068-2.29510.23131350.182261099
2.2951-2.39960.21551250.1776262398
2.3996-2.52610.2131560.1823258399
2.5261-2.68430.20631400.1804262499
2.6843-2.89160.21571490.1771261398
2.8916-3.18250.19881480.17312652100
3.1825-3.64280.19911510.1639267199
3.6428-4.58890.13911430.1489267498
4.5889-45.2790.22251710.1832277498
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)
18.4446-4.6293-3.0338.20943.33196.83270.0852-0.0868-0.8656-0.18910.16480.52660.2142-0.0541-0.19240.2534-0.0803-0.05510.33730.0850.365731.1472-17.5241-6.0253
26.3071.98973.88524.44692.06825.9141-0.0993-0.57060.42350.3016-0.11230.4172-0.3666-0.17970.23730.24630.03010.09450.2606-0.0490.30310.7562-1.3065-12.0188
32.31390.21940.31584.23151.24612.678-0.0673-0.1819-0.30530.1759-0.02720.32720.0822-0.14460.04670.1594-0.00060.06290.17740.02090.32053.7185-16.5383-15.8126
43.8423-1.31581.17034.3045-1.14121.82990.0830.303-0.332-0.1105-0.11910.10070.11630.08710.03430.15850.00150.02830.191-0.05750.238710.8925-17.9141-25.2681
53.95040.83331.5292.87190.04654.3116-0.16850.02950.55710.0474-0.00040.0123-0.37870.30090.20560.2472-0.0089-0.00580.19360.00990.336912.23562.5797-19.5469
63.84382.2237-3.07418.0001-2.81967.0524-0.204-0.39380.40210.740.1659-0.5774-0.75630.26040.1010.2906-0.013-0.05150.1809-0.08280.370512.74383.6667-10.0431
77.75153.4819-3.02926.8162-2.36683.31470.1441-0.6029-0.41410.6024-0.232-0.60810.00980.0710.10460.2521-0.0509-0.09530.31460.05120.231245.1365-6.8358-3.5983
85.8844-0.366-1.53995.12370.46333.69870.3225-0.524-0.49750.6677-0.24650.24930.1312-0.0259-0.06180.2944-0.0655-0.1030.35840.05930.186435.6303-7.0515-0.8183
92.4768-3.9146-0.94156.37272.10562.48530.2086-0.17890.2734-0.0444-0.2534-1.40070.08440.29660.04820.2313-0.03470.00560.41870.09360.490357.98790.9261-13.7452
102.1043.0497-2.70818.1286-1.62225.3120.06280.04440.28980.0950.0880.23910.025-0.1548-0.14250.2128-0.0438-0.01220.25420.04960.269437.59584.235-9.278
115.1274-0.0673-0.71512.9590.21381.5451-0.11960.76360.3856-0.38040.07850.0779-0.1269-0.08680.01610.2592-0.0841-0.01550.37060.08290.252939.46275.5602-19.1984
129.20321.8532-2.59072.19430.22485.1182-0.25770.462-1.3348-0.06760.0825-0.61640.5229-0.00940.15360.3096-0.05490.03790.2707-0.07850.501343.7754-12.7318-15.7241
135.90881.07722.37476.89971.14216.336-0.04910.5459-0.6817-0.04940.2060.14730.0017-0.5458-0.04870.1799-0.072-0.03850.2893-0.02050.372726.9023-13.2195-12.0326
143.6925-0.2658-3.26874.6819-0.38983.0972-0.0534-1.2004-0.84510.4942-0.443-0.05730.73060.75990.56530.368-0.0246-0.03530.50010.11390.422225.2439-21.6264-10.8272
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'B' and (resid 226 through 241 )B226 - 241
2X-RAY DIFFRACTION2chain 'A' and (resid 1 through 38 )A1 - 38
3X-RAY DIFFRACTION3chain 'A' and (resid 39 through 91 )A39 - 91
4X-RAY DIFFRACTION4chain 'A' and (resid 92 through 164 )A92 - 164
5X-RAY DIFFRACTION5chain 'A' and (resid 165 through 227 )A165 - 227
6X-RAY DIFFRACTION6chain 'A' and (resid 228 through 242 )A228 - 242
7X-RAY DIFFRACTION7chain 'B' and (resid 1 through 27 )B1 - 27
8X-RAY DIFFRACTION8chain 'B' and (resid 28 through 55 )B28 - 55
9X-RAY DIFFRACTION9chain 'B' and (resid 56 through 66 )B56 - 66
10X-RAY DIFFRACTION10chain 'B' and (resid 67 through 83 )B67 - 83
11X-RAY DIFFRACTION11chain 'B' and (resid 84 through 164 )B84 - 164
12X-RAY DIFFRACTION12chain 'B' and (resid 165 through 192 )B165 - 192
13X-RAY DIFFRACTION13chain 'B' and (resid 193 through 211 )B193 - 211
14X-RAY DIFFRACTION14chain 'B' and (resid 212 through 225 )B212 - 225

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