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- PDB-2jwl: Solution Structure of periplasmic domain of TolR from H. influenz... -

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Basic information

Entry
Database: PDB / ID: 2jwl
TitleSolution Structure of periplasmic domain of TolR from H. influenzae with SAXS data
ComponentsProtein tolR
KeywordsMEMBRANE PROTEIN / PROTEIN / Periplasmic domain / membrane / Inner membrane / Protein transport / Transmembrane / Transport
Function / homology
Function and homology information


transmembrane transporter activity / protein transport / cell division / plasma membrane
Similarity search - Function
Nucleotidyltransferase; domain 5 - #270 / Tol-Pal system protein TolR / Biopolymer transport protein ExbD/TolR / Biopolymer transport protein ExbD/TolR / Nucleotidyltransferase; domain 5 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Tol-Pal system protein TolR
Similarity search - Component
Biological speciesHaemophilus influenzae (bacteria)
MethodSOLUTION NMR / simulated annealing
AuthorsParsons, L.M. / Bax, A. / Grishaev, A.
CitationJournal: Biochemistry / Year: 2008
Title: The Periplasmic Domain of TolR from Haemophilus influenzae Forms a Dimer with a Large Hydrophobic Groove: NMR Solution Structure and Comparison to SAXS Data.
Authors: Parsons, L.M. / Grishaev, A. / Bax, A.
History
DepositionOct 15, 2007Deposition site: BMRB / Processing site: RCSB
Revision 1.0Apr 1, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 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 1.3May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein tolR
B: Protein tolR


Theoretical massNumber of molelcules
Total (without water)16,0122
Polymers16,0122
Non-polymers00
Water00
1


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

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Components

#1: Protein Protein tolR


Mass: 8006.144 Da / Num. of mol.: 2 / Fragment: periplasmic domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haemophilus influenzae (bacteria)
Description: the vector was modified to include a native E.coli GST-tag.
Gene: tolR / Plasmid: pet28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-star-(DE3) / References: UniProt: P43769

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1313D CBCA(CO)NH
1413D C(CO)NH
1513D HNCO
1613D HN(CA)CB
1713D 1H-15N NOESY
1813D H(CCO)NH
1913D 1H-13C NOESY
11013D HN(CO)CA
11113D HNCO-QJ

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Sample preparation

DetailsContents: 0.5-1.0 mM [U-99% 13C; U-99% 15N] TolR, 50 mM sodium phosphate, 50-100 mM sodium chloride, 0.05 mM EDTA, 93% H2O/7% D2O
Solvent system: 93% H2O/7% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMTolR[U-99% 13C; U-99% 15N]1
50 mMsodium phosphate1
50 mMsodium chloride1
0.05 mMEDTA1
5 %D2O1
Sample conditionspH: 6.7 / Pressure: ambient / Temperature: 303 K

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NMR measurement

NMR spectrometerType: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
SparkyGoddard, T.D. et al.peak picking
SparkyGoddard, T.D. et al.data analysis
CNS1.1Brunger, A.T. et al.refinement
NMRPipeDelaglio, F. et al.processing
TALOSCornilescu, G. et al.dihedral angle prediction
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: all calculated structures submitted
Conformers calculated total number: 20 / Conformers submitted total number: 20

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