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- PDB-2m8c: The solution NMR structure of E. coli apo-HisJ -

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Basic information

Entry
Database: PDB / ID: 2m8c
TitleThe solution NMR structure of E. coli apo-HisJ
ComponentsCationic amino acid ABC transporter, periplasmic binding protein
KeywordsTRANSPORT PROTEIN / Periplasmic binding protein / HisJ / apo
Function / homologyPeriplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta / :
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model1
AuthorsChu, B.C.H. / Vogel, H.J.
CitationJournal: J.Biol.Chem. / Year: 2013
Title: Role of the Two Structural Domains from the Periplasmic Escherichia coli Histidine-binding Protein HisJ.
Authors: Chu, B.C. / Dewolf, T. / Vogel, H.J.
History
DepositionMay 15, 2013Deposition site: BMRB / Processing site: RCSB
Revision 1.0Oct 2, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2013Group: Database references
Revision 1.2Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.3Oct 16, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cationic amino acid ABC transporter, periplasmic binding protein


Theoretical massNumber of molelcules
Total (without water)26,5101
Polymers26,5101
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)30 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Cationic amino acid ABC transporter, periplasmic binding protein / Histidine/lysine/arginine/ornithine transporter subunit


Mass: 26509.869 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: hisJ, EcDH1_1347, ECDH1ME8569_2247 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: C9QQM5
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1123D 1H-15N NOESY
1233D 1H-13C NOESY
1313D HN(CA)CB
1413D CBCA(CO)NH
1513D HNCO
1612D 1H-15N HSQC

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Sample preparation

Details
Solution-IDContentsSolvent system
11 mM [U-13C; U-15N; U-2H] apo-HisJ, 50 mM sodium phosphate, 10 % D2O, 90 % H2O, 0.5 mM DSS, 90% H2O/10% D2O90% H2O/10% D2O
21 mM [U-13C; U-15N] apo-HisJ, 50 mM sodium phosphate, 10 % D2O, 90 % H2O, 0.5 mM DSS, 90% H2O/10% D2O90% H2O/10% D2O
31 mM [U-13C; U-15N] apo-HisJ, 50 mM sodium phosphate, 100 % D2O, 0.5 mM DSS, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMapo-HisJ-1[U-13C; U-15N; U-2H]1
50 mMsodium phosphate-21
10 %D2O-31
90 %H2O-41
0.5 mMDSS-51
1 mMapo-HisJ-6[U-13C; U-15N]2
50 mMsodium phosphate-72
10 %D2O-82
90 %H2O-92
0.5 mMDSS-102
1 mMapo-HisJ-11[U-13C; U-15N]3
50 mMsodium phosphate-123
100 %D2O-133
0.5 mMDSS-143
Sample conditionsIonic strength: 0 / pH: 7 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 700 MHz

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Processing

NMR software
NameDeveloperClassification
NMRDrawDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
SparkyGoddardpeak picking
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure solution
X-PLOR NIHrefinement
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: 30

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