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- PDB-2jok: NMR structure of the catalytic domain of guanine nucleotide excha... -

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Basic information

Entry
Database: PDB / ID: 2jok
TitleNMR structure of the catalytic domain of guanine nucleotide exchange factor BopE from Burkholderia pseudomallei
ComponentsPutative G-nucleotide exchange factor
KeywordsCELL INVASION / SIGNALING PROTEIN / Guanine nucleotide exchange factor / Burkholderia pseudomallei / Type III secretion / SopE / SopE2
Function / homology
Function and homology information


GTPase activator activity / guanyl-nucleotide exchange factor activity / actin cytoskeleton organization / extracellular region
Similarity search - Function
SopE-like, GEF domain / Guanine nucleotide exchange factor SopE / Guanine nucleotide exchange factor SopE, GEF domain / SopE-like, GEF domain superfamily / SopE GEF domain / SopE-like GEF fold / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Guanine nucleotide exchange factor BopE
Similarity search - Component
Biological speciesBurkholderia pseudomallei (bacteria)
MethodSOLUTION NMR / simulated annealing
Model detailsSolution structure of BopE
AuthorsWu, H. / Upadhyay, A. / Williams, C. / Galyov, E.E. / van den Elsen, J.M.H. / Bagby, S.
CitationJournal: Biochem.J. / Year: 2008
Title: The guanine-nucleotide-exchange factor BopE from Burkholderia pseudomallei adopts a compact version of the Salmonella SopE/SopE2 fold and undergoes a closed-to-open conformational change upon ...Title: The guanine-nucleotide-exchange factor BopE from Burkholderia pseudomallei adopts a compact version of the Salmonella SopE/SopE2 fold and undergoes a closed-to-open conformational change upon interaction with Cdc42
Authors: Upadhyay, A. / Wu, H.L. / Williams, C. / Field, T. / Galyov, E.E. / van den Elsen, J.M. / Bagby, S.
History
DepositionMar 14, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 18, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 9, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
Revision 1.3Dec 20, 2023Group: Data collection / Other
Category: chem_comp_atom / chem_comp_bond / pdbx_database_status
Item: _pdbx_database_status.deposit_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative G-nucleotide exchange factor


Theoretical massNumber of molelcules
Total (without water)20,1361
Polymers20,1361
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 / 40structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein Putative G-nucleotide exchange factor


Mass: 20136.344 Da / Num. of mol.: 1 / Fragment: residues 78-261
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia pseudomallei (bacteria) / Gene: bopE / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q63K41

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR / Details: Solution structure of BopE
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1312D 1H-1H TOCSY
1412D 1H-1H NOESY
1513D CBCA(CO)NH
1613D C(CO)NH
1713D HNCO
1813D HNCA
1913D HN(CA)CB
11013D HBHA(CO)NH
11113D HN(CO)CA
11213D H(CCO)NH
11313D (H)CCH-TOCSY
11413D (H)CCH-TOCSY
11513D HNHA
11613D 1H-15N NOESY
11713D 1H-15N TOCSY
11813D 1H-13C NOESY
1191IPAP-HSQC

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Sample preparation

DetailsContents: 0.8 mM protein, 20 mM potassium phosphate, 50 mM sodium chloride, 10 mM DTT, 1 mM benzamidine, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentSolution-ID
20 mMpotassium phosphate1
50 mMsodium chloride1
10 mMDTT1
1 mMbenzamidine1
Sample conditionsIonic strength: 100 / pH: 5.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

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Processing

NMR software
NameDeveloperClassification
SparkyGoddarddata analysis
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure solution
TALOSCornilescu, Delaglio and Baxdata analysis
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 40 / Conformers submitted total number: 20

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