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- PDB-2h3k: Solution Structure of the first NEAT domain of IsdH -

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Basic information

Entry
Database: PDB / ID: 2h3k
TitleSolution Structure of the first NEAT domain of IsdH
ComponentsHaptoglobin-binding surface anchored protein
KeywordsPROTEIN BINDING / NEAT domain / IsdH / HarA
Function / homology
Function and homology information


heme binding / extracellular region
Similarity search - Function
Iron-regulated surface determinant protein H / : / Iron-regulated surface determinant protein H/B, linker domain / Immunoglobulin-like - #1850 / NEAT domain / Iron Transport-associated domain / NEAT domain profile. / NEAr Transporter domain / NEAT domain superfamily / YSIRK Gram-positive signal peptide ...Iron-regulated surface determinant protein H / : / Iron-regulated surface determinant protein H/B, linker domain / Immunoglobulin-like - #1850 / NEAT domain / Iron Transport-associated domain / NEAT domain profile. / NEAr Transporter domain / NEAT domain superfamily / YSIRK Gram-positive signal peptide / Gram-positive cocci surface proteins LPxTG motif profile. / LPXTG cell wall anchor domain / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Iron-regulated surface determinant protein H
Similarity search - Component
Biological speciesStaphylococcus aureus subsp. aureus (bacteria)
MethodSOLUTION NMR / distance geometry
AuthorsPilpa, R.M. / Fadeev, E.A. / Villareal, V.A. / Wong, M.A. / Phillips, M. / Clubb, R.T.
CitationJournal: J.Mol.Biol. / Year: 2006
Title: Solution structure of the NEAT (NEAr Transporter) domain from IsdH/HarA: the human hemoglobin receptor in Staphylococcus aureus.
Authors: Pilpa, R.M. / Fadeev, E.A. / Villareal, V.A. / Wong, M.L. / Phillips, M. / Clubb, R.T.
History
DepositionMay 22, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 22, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Feb 19, 2020Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 1.4Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Haptoglobin-binding surface anchored protein


Theoretical massNumber of molelcules
Total (without water)16,7331
Polymers16,7331
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 / 200structures with acceptable covalent geometry,structures with favorable non-bond energy,structures with the least restraint violations,structures with the lowest energy
RepresentativeModel #1fewest violations,lowest energy,minimized average structure

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Components

#1: Protein Haptoglobin-binding surface anchored protein


Mass: 16733.449 Da / Num. of mol.: 1 / Fragment: First neat domain, IsdH-N1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus subsp. aureus (bacteria)
Species: Staphylococcus aureus / Strain: MSSA476 / Gene: SA1552 / Plasmid: pet11a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q6G8J7

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
1223D 13C-separated NOESY
1333D 13C-separated NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
1Uniform labeling with 15N at 1mM in 50mM sodium phosphate pH 6.0 and 100mM NaCl93% H2O and 7%D2O
2Uniform labeling with 13C/15N at 1mM in 50mM sodium phosphate pH 6.0 and 100mM NaCl with 7% D2O93% H2O and 7%D2O
3Uniform labeling with 13C/15N at 1mM in 50mM sodium phosphate pH 6.0 and 100mM NaCl100% D2O
Sample conditionsIonic strength: 100mM NaCl / pH: 6.0 / Pressure: ambient / Temperature: 295 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE6001
Bruker AVANCEBrukerAVANCE6002
Bruker AVANCEBrukerAVANCE6003

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipe4.3.5Delagliodata analysis
NMRView5.2Blevins and Garrettdata analysis
XwinNMR3.5collection
RefinementMethod: distance geometry / Software ordinal: 1
Details: 1841 experimentally derived restraints (1741 NOE-derived distance constraints, 64 dihedral angle restraints, 40 hydrogen bond restraints)
NMR representativeSelection criteria: fewest violations,lowest energy,minimized average structure
NMR ensembleConformer selection criteria: structures with acceptable covalent geometry,structures with favorable non-bond energy,structures with the least restraint violations,structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20

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