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- PDB-9bch: Solution structure of the hemoglobin receptor HbpA from Corynebac... -

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Basic information

Entry
Database: PDB / ID: 9bch
TitleSolution structure of the hemoglobin receptor HbpA from Corynebacterium diphtheriae
ComponentsMembrane protein
KeywordsPROTEIN BINDING / receptor / capping / beta-sandwich
Function / homologymembrane / Membrane protein
Function and homology information
Biological speciesCorynebacterium diphtheriae NCTC 13129 (bacteria)
MethodSOLUTION NMR / simulated annealing
AuthorsMahoney, B.J. / Clubb, R.T.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01-AI161828 United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2025
Title: Molecular basis of hemoglobin binding and heme removal in Corynebacterium diphtheriae.
Authors: Mahoney, B.J. / Lyman, L.R. / Ford, J. / Soule, J. / Cheung, N.A. / Goring, A.K. / Ellis-Guardiola, K. / Collazo, M.J. / Cascio, D. / Ton-That, H. / Schmitt, M.P. / Clubb, R.T.
History
DepositionApr 9, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 8, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Membrane protein


Theoretical massNumber of molelcules
Total (without water)21,9191
Polymers21,9191
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, NMR relaxation study
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Membrane protein


Mass: 21918.514 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: A31S, TEV cleavage scar
Source: (gene. exp.) Corynebacterium diphtheriae NCTC 13129 (bacteria)
Gene: DIP2330 / Plasmid: pMAPLe4 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q6NEE5
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
122isotropic12D 1H-15N HSQC
133isotropic22D 1H-13C HSQC aliphatic
143isotropic22D 1H-13C HSQC aromatic
112isotropic13D HNCO
152isotropic13D HNCA
1102isotropic13D HN(CO)CA
192isotropic13D HN(CA)CB
182isotropic13D CBCA(CO)NH
173isotropic23D (H)CCH-COSY
163isotropic23D (H)CCH-TOCSY
1142isotropic33D H(CCO)NH
1132isotropic33D 1H-15N TOCSY
1122isotropic13D 1H-13C NOESY aliphatic
1113isotropic23D 1H-13C NOESY aliphatic
1153isotropic23D 1H-13C NOESY aromatic
1162isotropic13D 1H-15N NOESY
1172isotropic13D HBHA(CO)NH

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution20.72 mM [U-100% 13C; U-100% 15N] Hemoglobin receptor HbpA, 50 mM sodium phosphate, 100 mM sodium chloride, 90% H2O/10% D2O15N_13C_H2O_sample90% H2O/10% D2O
solution30.72 mM [U-100% 13C; U-100% 15N] Hemoglobin receptor HbpA, 50 mM sodium phosphate, 100 mM sodium chloride, 100% D2O15N_13C_D2O_sample100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.72 mMHemoglobin receptor HbpA[U-100% 13C; U-100% 15N]2
50 mMsodium phosphatenatural abundance2
100 mMsodium chloridenatural abundance2
0.72 mMHemoglobin receptor HbpA[U-100% 13C; U-100% 15N]3
50 mMsodium phosphatenatural abundance3
100 mMsodium chloridenatural abundance3
Sample conditionsIonic strength: 100 mM / Label: HbpA_conditions / pH: 7.2 / Pressure: 1 atm / Temperature: 295 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE III HDBrukerAVANCE III HD6001
Bruker AVANCE NEOBrukerAVANCE NEO8002
Bruker AVANCE DRXBrukerAVANCE DRX5003

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Processing

NMR software
NameVersionDeveloperClassification
CARA1.9.1.7Keller and Wuthrichchemical shift assignment
X-PLOR NIH3.6Schwieters, Kuszewski, Tjandra and Clorestructure calculation
X-PLOR NIH3.6Schwieters, Kuszewski, Tjandra and Clorerefinement
Xipp1.21.7Dan Garrettpeak picking
Xipp1.21.7Dan Garrettchemical shift assignment
UNIO10Torsten Herrmannstructure calculation
TopSpinBruker Biospincollection
NMRPipe11.1Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRFAM-SPARKYNational Magnetic Resonance Facility at Madison (Wisconsin)data analysis
TALOS-NCornilescu, Delaglio and Baxgeometry optimization
PROCHECK / PROCHECK-NMRLaskowski, MacArthur, Smith, Jones, Hutchinson, Morris, Moss and Thorntongeometry optimization
RefinementMethod: simulated annealing / Software ordinal: 3
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20

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