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- PDB-2m5j: Solution structure of the periplasmic signaling domain of HasR, a... -

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Basic information

Entry
Database: PDB / ID: 2m5j
TitleSolution structure of the periplasmic signaling domain of HasR, a TonB-dependent outer membrane heme transporter
ComponentsHasR protein
KeywordsSIGNALING PROTEIN / signaling domain / TonB dependent transporter
Function / homology
Function and homology information


heme transmembrane transporter activity / cell outer membrane / metal ion binding
Similarity search - Function
TonB-dependent haem/haemoglobin receptor / TonB-dependent haemoglobin/transferrin/lactoferrin receptor / Phage tail protein beta-alpha-beta fold - #30 / Phage tail protein beta-alpha-beta fold / Secretin and TonB N terminus short domain / Secretin/TonB, short N-terminal domain / Secretin and TonB N terminus short domain / Vitamin B12 transporter BtuB-like / TonB-dependent receptor-like, beta-barrel / TonB dependent receptor ...TonB-dependent haem/haemoglobin receptor / TonB-dependent haemoglobin/transferrin/lactoferrin receptor / Phage tail protein beta-alpha-beta fold - #30 / Phage tail protein beta-alpha-beta fold / Secretin and TonB N terminus short domain / Secretin/TonB, short N-terminal domain / Secretin and TonB N terminus short domain / Vitamin B12 transporter BtuB-like / TonB-dependent receptor-like, beta-barrel / TonB dependent receptor / TonB-dependent receptor, plug domain superfamily / TonB-dependent receptor, plug domain / TonB-dependent receptor-like, beta-barrel domain superfamily / TonB-dependent Receptor Plug Domain / 3-Layer(bab) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesSerratia marcescens (bacteria)
MethodSOLUTION NMR / simulated annealing, torsion angle dynamics
Model detailsrepresentative secondary structure, model6
AuthorsMalki, I. / Cardoso de Amorim, G. / Prochnicka-Chalufour, A. / Simenel, C. / Delepierre, M. / Izadi-Pruneyre, N.
CitationJournal: Plos One / Year: 2014
Title: Interaction of a Partially Disordered Antisigma Factor with Its Partner, the Signaling Domain of the TonB-Dependent Transporter HasR
Authors: Malki, I. / Simenel, C. / Wojtowicz, H. / Cardoso de Amorim, G. / Prochnicka-Chalufour, A. / Hoos, S. / Raynal, B. / England, P. / Chaffotte, A. / Delepierre, M. / Delepelaire, P. / Izadi-Pruneyre, N.
History
DepositionFeb 26, 2013Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Mar 5, 2014Provider: repository / Type: Initial release
Revision 1.1Apr 23, 2014Group: 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 / 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 / _struct_ref_seq_dif.details
Revision 1.3May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HasR protein


Theoretical massNumber of molelcules
Total (without water)11,1071
Polymers11,1071
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 / 400structures with the lowest energy
RepresentativeModel #1representative secondary structure

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Components

#1: Protein HasR protein


Mass: 11106.586 Da / Num. of mol.: 1 / Fragment: UNP residues 42-146
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Serratia marcescens (bacteria) / Gene: hasR / Production host: Escherichia coli (E. coli) / References: UniProt: Q79AD2

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR / Details: HasR N-terminal periplasmic signaling domain
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1313D CBCA(CO)NH
1413D HN(CA)CB
1513D HNCO
1613D C(CO)NH
1713D H(CCO)NH
1813D (H)CCH-TOCSY
1912D (HB)CB(CGCD)HD
11012D (HB)CB(CGCDCE)HE
11113D 1H-15N NOESY
11213D 1H-13C NOESY aliphatic
11313D 1H-13C NOESY aromatic

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Sample preparation

DetailsContents: 0.5 mM [U-99% 13C; U-99% 15N] HasR_N-terminal_periplasmic_signaling_domain-1, 50 mM Sodium phosphate-2, 50 mM NaCl-3, 85% H2O/15% D2O
Solvent system: 85% H2O/15% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMHasR_N-terminal_periplasmic_signaling_domain-1[U-99% 13C; U-99% 15N]1
50 mMSodium phosphate-21
50 mMNaCl-31
Sample conditionsIonic strength: 0.1 / pH: 7.0 / Pressure: 1 atm / Temperature: 293 K

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NMR measurement

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

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Processing

NMR software
NameVersionDeveloperClassification
CcpNmr Analysis2.15CCPNchemical shift assignment
CNS1.2Brunger, Adams, Clore, Gros, Nilges and Readstructure solution
ARIA2.3Linge, O'Donoghue and Nilgesstructure solution
ARIA2.3Linge, O'Donoghue and Nilgesrefinement
CNSrefinement
RefinementMethod: simulated annealing, torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: representative secondary structure
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 400 / Conformers submitted total number: 20 / Representative conformer: 6

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