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- PDB-2k78: Solution Structure of the IsdC NEAT domain bound to Zinc Protopor... -

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Basic information

Entry
Database: PDB / ID: 2k78
TitleSolution Structure of the IsdC NEAT domain bound to Zinc Protoporphyrin
ComponentsIron-regulated surface determinant protein C
KeywordsHEME-BINDING PROTEIN / NEAT domain / NMR complex / heme / Isd / IsdC / Cell wall / Iron / Metal-binding / Peptidoglycan-anchor / Secreted / TRANSPORT PROTEIN
Function / homology
Function and homology information


heme transport / hemoglobin binding / peptidoglycan-based cell wall / extracellular region / metal ion binding
Similarity search - Function
Sortase B signal domain, NPQTN class / Haem uptake protein IsdC / Immunoglobulin-like - #1850 / NEAT domain / Iron Transport-associated domain / NEAT domain profile. / NEAr Transporter domain / NEAT domain superfamily / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING ZN / Iron-regulated surface determinant protein C
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodSOLUTION NMR / simulated annealing
AuthorsVillareal, V.A. / Pilpa, R.M. / Robson, S.A. / Fadeev, E.A. / Clubb, R.T.
CitationJournal: J.Biol.Chem. / Year: 2008
Title: The IsdC Protein from Staphylococcus aureus Uses a Flexible Binding Pocket to Capture Heme.
Authors: Villareal, V.A. / Pilpa, R.M. / Robson, S.A. / Fadeev, E.A. / Clubb, R.T.
History
DepositionAug 6, 2008Deposition site: BMRB / Processing site: RCSB
Revision 1.0Aug 19, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3May 22, 2024Group: Data collection
Category: chem_comp_atom / chem_comp_bond / pdbx_validate_chiral

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Iron-regulated surface determinant protein C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,2512
Polymers16,6251
Non-polymers6261
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)30 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Iron-regulated surface determinant protein C / Staphylococcal iron-regulated protein D


Mass: 16625.418 Da / Num. of mol.: 1 / Fragment: NEAT domain, UNP residues 25-150
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (strain MW2) (bacteria)
Gene: isdC, sirD, MW1013 / Production host: Escherichia coli (E. coli) / References: UniProt: Q7A151
#2: Chemical ChemComp-ZNH / PROTOPORPHYRIN IX CONTAINING ZN


Mass: 626.051 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32N4O4Zn

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1222D 1H-13C HSQC
1313D CBCA(CO)NH
1413D HN(CA)CB
1513D HNCA
1613D HNHA
1723D (H)CCH-COSY
1823D (H)CCH-TOCSY
1913D 1H-15N NOESY
11013D HNCO
11113D HNHB

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Sample preparation

Details
Solution-IDContentsSolvent system
150 mM sodium phosphate, 100 mM sodium chloride, 0.01 % sodium azide, 1.3 mM [U-100% 13C; U-100% 15N] IsdC, 2.1 mM PROTOPORPHYRIN IX CONTAINING ZN, 7 % [U-100% 2H] D2O, 93% H2O/7% D2O93% H2O/7% D2O
250 mM sodium phosphate, 100 mM sodium chloride, 0.01 % sodium azide, 1.1 mM IsdC, 2.3 mM PROTOPORPHYRIN IX CONTAINING ZN, 100 % D2O, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
50 mMsodium phosphate1
100 mMsodium chloride1
0.01 %sodium azide1
1.3 mMIsdC[U-100% 13C; U-100% 15N]1
2.1 mMPROTOPORPHYRIN IX CONTAINING ZN1
7 %D2O[U-100% 2H]1
50 mMsodium phosphate2
100 mMsodium chloride2
0.01 %sodium azide2
1.1 mMIsdC2
2.3 mMPROTOPORPHYRIN IX CONTAINING ZN2
100 %D2O2
Sample conditionsIonic strength: 0.15 / pH: 6 / Pressure: ambient / Temperature: 302 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE5001
Bruker AvanceBrukerAVANCE6002
Bruker AvanceBrukerAVANCE8003

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Processing

NMR software
NameDeveloperClassification
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
PIPPGarrettpeak picking
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
ATNOS/CANDIDHerrmann, Guntert, Wuthrichchemical shift assignment
CARAKellerchemical shift assignment
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 30

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