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- PDB-2m2k: The structure of HasB CTD -

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Basic information

Entry
Database: PDB / ID: 2m2k
TitleThe structure of HasB CTD
ComponentsHasB protein
KeywordsTRANSPORT PROTEIN / HasB CTD / tonb-like protein / hemophore / HEME acquisition system
Function / homology
Function and homology information


transmembrane transport / membrane => GO:0016020 / plasma membrane
Similarity search - Function
Fusion Protein Consisting Of Minor Coat Protein, Glycine Rich Linker, Tola, And A His Tag; Chain: A; Domain 2 / Fusion Protein Consisting Of Minor Coat Protein, Glycine Rich Linker, Tola, And A His Tag; Chain: A; Domain 2 - #10 / TonB, C-terminal / Gram-negative bacterial TonB protein C-terminal / TonB/TolA, C-terminal / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesSerratia marcescens (bacteria)
MethodSOLUTION NMR / simulated annealing, molecular dynamics
Model detailslowest energy, model 1
AuthorsProchnicka-Chalufour, A. / Lefevre, J. / Simenel, C. / Delepelaire, P. / Wandersman, C. / Delepierre, M. / Izadi-Pruneyre, N.
CitationJournal: Plos One / Year: 2013
Title: The Structure of HasB Reveals a New Class of TonB Protein Fold.
Authors: de Amorim, G.C. / Prochnicka-Chalufour, A. / Delepelaire, P. / Lefevre, J. / Simenel, C. / Wandersman, C. / Delepierre, M. / Izadi-Pruneyre, N.
History
DepositionDec 26, 2012Deposition site: BMRB / Processing site: RCSB
Revision 1.0Apr 10, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status / pdbx_nmr_software
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HasB protein


Theoretical massNumber of molelcules
Total (without water)14,2941
Polymers14,2941
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 / 500structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein HasB protein


Mass: 14294.267 Da / Num. of mol.: 1 / Fragment: HasB C-terminal domain (UNP residues 133-263)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Serratia marcescens (bacteria) / Gene: hasB / Production host: Escherichia coli (E. coli) / References: UniProt: Q79AD1

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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 HBHA(CO)NH
1813D 1H-15N NOESY
1913D 1H-13C NOESY

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Sample preparation

DetailsContents: 0.8 mM [U-99% 13C; U-99% 15N] urea, 85% H2O/15% D2O
Solvent system: 85% H2O/15% D2O
SampleConc.: 0.8 mM / Component: urea-1 / Isotopic labeling: [U-99% 13C; U-99% 15N]
Sample conditionsIonic strength: 0.5 / pH: 7.0 / Pressure: ambient / Temperature: 293 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
VnmrJ3.2Agilent Technologiesdata acquisition
VnmrJ3.2Agilent Technologiesdata processing
CNS_1.2Brunger, Adams, Clore, Gros, Nilges and Readstructure solution
Aria_2.2Linge, O'Donoghue and Nilgesstructure solution
XEASYBartels et al.data analysis
Aria_2.2refinement
CNS_1.2Brunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: simulated annealing, molecular dynamics / Software ordinal: 1
NMR constraintsNOE constraints total: 2117 / NOE intraresidue total count: 607 / NOE long range total count: 719 / NOE medium range total count: 303 / NOE sequential total count: 488 / Protein chi angle constraints total count: 0 / Protein other angle constraints total count: 0 / Protein phi angle constraints total count: 74 / Protein psi angle constraints total count: 74
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 500 / Conformers submitted total number: 20

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