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- PDB-2kil: NMR structure of the H103G mutant SO2144 H-NOX domain from Shewan... -

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Basic information

Entry
Database: PDB / ID: 2kil
TitleNMR structure of the H103G mutant SO2144 H-NOX domain from Shewanella oneidensis in the Fe(II)CO ligation state
ComponentsPutative uncharacterized protein
KeywordsUNKNOWN FUNCTION / H-NOX
Function / homology
Function and homology information


heme binding / metal ion binding
Similarity search - Function
H-NOX domain / H-NOX domain / Heme NO-binding / H-NOX domain superfamily / Haem-NO-binding / NO signalling/Golgi transport ligand-binding domain superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
CARBON MONOXIDE / PROTOPORPHYRIN IX CONTAINING FE / IMIDAZOLE / NO-binding heme-dependent sensor protein
Similarity search - Component
Biological speciesShewanella oneidensis (bacteria)
MethodSOLUTION NMR / simulated annealing
AuthorsErbil, W.K.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2009
Title: A structural basis for H-NOX signaling in Shewanella oneidensis by trapping a histidine kinase inhibitory conformation.
Authors: Erbil, W.K. / Price, M.S. / Wemmer, D.E. / Marletta, M.A.
History
DepositionMay 6, 2009Deposition site: BMRB / Processing site: RCSB
Revision 1.0Nov 17, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 13, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn / 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_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,1674
Polymers20,4541
Non-polymers7143
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein Putative uncharacterized protein


Mass: 20453.500 Da / Num. of mol.: 1 / Mutation: H103G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shewanella oneidensis (bacteria) / Gene: SO2144, SO_2144 / Plasmid: pET20b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)PLysS / References: UniProt: Q8EF49
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-CMO / CARBON MONOXIDE


Mass: 28.010 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CO
#4: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D HNCA
1313D HNCO
1413D CBCA(CO)NH
1513D HBHA(CO)NH
1613D C(CO)NH
1723D (H)CCH-TOCSY
1823D (H)CCH-COSY
1913D 1H-13C NOESY
11023D 1H-13C NOESY
11133D 1H-15N NOESY
11233D 1H-15N TOCSY
11322D 1H-13C HSQC

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Sample preparation

Details
Solution-IDContentsSolvent system
10.4-0.8 mM [U-99% 13C; U-99% 15N] H-NOX, DTT, glycerol, imidazole, 90% H2O, 10% D2O90% H2O/10% D2O
20.4-0.8 mM [U-99% 13C; U-99% 15N] H-NOX, DTT, glycerol, imidazole, 100% D2O100% D2O
30.4-0.8 mM [U-99% 15N] H-NOX, DTT, glycerol, imidazole, 90% H2O/10% D2O90% H2O/10% D2O
Sample
UnitsComponentIsotopic labelingConc. range (mg/ml)Solution-ID
mMH-NOX, DTT, glycerol, imidazole[U-99% 13C; U-99% 15N]0.4-0.81
mMH-NOX, DTT, glycerol, imidazole[U-99% 13C; U-99% 15N]0.4-0.82
mMH-NOX, DTT, glycerol, imidazole[U-99% 15N]0.4-0.83
Sample conditionsIonic strength: 50 / pH: 7.4 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX9001
Bruker DRXBrukerDRX8002
Bruker DRXBrukerDRX6003
Bruker DRXBrukerDRX5004

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Processing

NMR softwareName: XPLOR-NIH / Developer: Schwieters, C.D. et al. / Classification: refinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20

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