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- PDB-2kkx: Solution Structure of C-terminal domain of reduced NleG2-3 (resid... -

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Basic information

Entry
Database: PDB / ID: 2kkx
TitleSolution Structure of C-terminal domain of reduced NleG2-3 (residues 90-191) from Pathogenic E. coli O157:H7. Northeast Structural Genomics Consortium and Midwest Center for Structural Genomics target ET109A
ComponentsUncharacterized protein ECs2156
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / Methods Development / U-box domain / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG / Ontario Centre for Structural Proteomics / OCSP / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


biological process involved in symbiotic interaction / ubiquitin-protein transferase activity
Similarity search - Function
Effector protein NleG / Effector protein NleG / Effector protein NleG superfamily / Effector protein NleG / Herpes Virus-1 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
T3SS secreted effector NleG
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 1
AuthorsWu, B. / Yee, A. / Fares, C. / Lemak, A. / Semest, A. / Claude, M. / Singer, A. / Edwards, A. / Savchenko, A. / Montelione, G.T. ...Wu, B. / Yee, A. / Fares, C. / Lemak, A. / Semest, A. / Claude, M. / Singer, A. / Edwards, A. / Savchenko, A. / Montelione, G.T. / Joachimiak, A. / Arrowsmith, C.H. / Northeast Structural Genomics Consortium (NESG) / Ontario Centre for Structural Proteomics (OCSP) / Midwest Center for Structural Genomics (MCSG)
Citation
Journal: Plos Pathog. / Year: 2010
Title: NleG Type 3 effectors from enterohaemorrhagic Escherichia coli are U-Box E3 ubiquitin ligases.
Authors: Wu, B. / Skarina, T. / Yee, A. / Jobin, M.C. / Dileo, R. / Semesi, A. / Fares, C. / Lemak, A. / Coombes, B.K. / Arrowsmith, C.H. / Singer, A.U. / Savchenko, A.
#1: Journal: J.Biomol.Nmr / Year: 2011
Title: A novel strategy for NMR resonance assignment and protein structure determination.
Authors: Lemak, A. / Gutmanas, A. / Chitayat, S. / Karra, M. / Fares, C. / Sunnerhagen, M. / Arrowsmith, C.H.
History
DepositionJun 29, 2009Deposition site: BMRB / Processing site: RCSB
Revision 1.0Aug 25, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jan 18, 2012Group: Database references
Revision 1.3Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.4Feb 26, 2020Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 1.5Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Uncharacterized protein ECs2156


Theoretical massNumber of molelcules
Total (without water)11,2911
Polymers11,2911
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Uncharacterized protein ECs2156


Mass: 11290.848 Da / Num. of mol.: 1 / Fragment: residues 90-191
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: O157:H7 / Gene: ECs2156, Z2149 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8X509

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR / Details: PSI Methods Development
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D HNCO
1213D CBCA(CO)NH
1313D HBHA(CO)NH
1413D HNCA
1513D (H)CCH-TOCSY
1613D CCH-TOCSY
1713D 1H-15N NOESY
1813D 1H-13C NOESY
1913D 1H-13C NOESY aromatic
11022D 1H-13C HSQC
11113D IPAP-J HNCO

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Sample preparation

Details
Solution-IDContentsSolvent system
10.5 mM [U-100% 13C; U-100% 15N] NleG, 10 mM [U-100% 2H] TRIS, 300 mM sodium chloride, 10 mM DTT, 1 mM benzamidine, 0.01 % sodium azide, 90% H2O/10% D2O90% H2O/10% D2O
20.5 mM [U-7% 13C; U-100% 15N] NleG, 10 mM [U-100% 2H] TRIS, 300 mM sodium chloride, 10 mM DTT, 1 mM benzamidine, 0.01 % sodium azide, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMNleG-1[U-100% 13C; U-100% 15N]1
10 mMTRIS-2[U-100% 2H]1
300 mMsodium chloride-31
10 mMDTT-41
1 mMbenzamidine-51
0.01 %sodium azide-61
0.5 mMNleG-7[U-7% 13C; U-100% 15N]2
10 mMTRIS-8[U-100% 2H]2
300 mMsodium chloride-92
10 mMDTT-102
1 mMbenzamidine-112
0.01 %sodium azide-122
Sample conditionsIonic strength: 300 / pH: 7.0 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE6001
Bruker AvanceBrukerAVANCE8002

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipe2.3Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
MDDGUI1Gutmanas and Arrowsmithprocessing
Sparky3.95Goddarddata analysis
Sparky3.95Goddardpeak picking
FAWN1Lemak and Arrowsmithchemical shift assignment
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
AutoStructureHuang, Tejero, Powers and Montelionenmr structure quality assessment
PSVSBhattacharya and Montelionenmr structure quality assessment
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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