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- PDB-2ru9: Structure of the YAM domain of E. coli Transporter YajR -

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Basic information

Entry
Database: PDB / ID: 2ru9
TitleStructure of the YAM domain of E. coli Transporter YajR
ComponentsPredicted transporter
KeywordsTRANSPORT PROTEIN / ferredoxin like
Function / homology
Function and homology information


transmembrane transporter activity / membrane => GO:0016020 / plasma membrane
Similarity search - Function
Major facilitator superfamily / Major Facilitator Superfamily / Alpha-Beta Plaits - #100 / Major facilitator superfamily domain / Major facilitator superfamily (MFS) profile. / MFS transporter superfamily / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Inner membrane transporter YajR
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model1
AuthorsLiu, X. / Feng, W.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2014
Title: Atomic resolution structure of the E. coli YajR transporter YAM domain.
Authors: Jiang, D. / Zhao, Y. / Fan, J. / Liu, X. / Wu, Y. / Feng, W. / Zhang, X.C.
History
DepositionFeb 27, 2014Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Jul 2, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 11, 2019Group: Data collection / Database references ...Data collection / Database references / Source and taxonomy / Structure summary
Category: entity_name_com / entity_src_gen ...entity_name_com / entity_src_gen / pdbx_nmr_software / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _entity_src_gen.gene_src_strain / _entity_src_gen.pdbx_beg_seq_num ..._entity_src_gen.gene_src_strain / _entity_src_gen.pdbx_beg_seq_num / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_seq_type / _pdbx_nmr_software.name / _struct_ref.db_code / _struct_ref.pdbx_db_accession / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq_dif.details / _struct_ref_seq_dif.pdbx_seq_db_accession_code
Revision 1.2Aug 24, 2022Group: Database references / Category: citation / database_2
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Jun 14, 2023Group: Other / Category: pdbx_database_status / Item: _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: Predicted transporter


Theoretical massNumber of molelcules
Total (without water)8,7051
Polymers8,7051
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 Predicted transporter / Inner membrane transporter YajR


Mass: 8704.834 Da / Num. of mol.: 1 / Fragment: YAM domain, UNP residues 389-454
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: yajR / Production host: Escherichia coli (E. coli) / References: UniProt: A0A066R7V5

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D HNCO
1313D HN(CA)CB
1413D CBCA(CO)NH
1512D 1H-13C HSQC
1613D C(CO)NH
1713D HBHA(CO)NH
1813D 1H-13C NOESY aliphatic
1913D 1H-15N NOESY
11013D 1H-13C NOESY aromatic

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Sample preparation

DetailsContents: 90 % H2O-1, 10 % D2O-2, 50 mM sodium phosphate-3, 1 mM EDTA-4, 1 mM DTT-5, 150 mM sodium chloride-6, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentSolution-ID
90 %H2O-11
10 %D2O-21
50 mMsodium phosphate-31
1 mMEDTA-41
1 mMDTT-51
150 mMsodium chloride-61
Sample conditionsIonic strength: 0.2 / pH: 6.3 / Pressure: ambient / Temperature: 303 K

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NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
ARIA2.3Linge, O'Donoghue and Nilgeschemical shift assignment
ARIA2.3Linge, O'Donoghue and Nilgesstructure solution
SparkyGoddarddata analysis
SparkyGoddardchemical shift assignment
SparkyGoddardpeak picking
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
ARIArefinement
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 / Representative conformer: 1

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