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- PDB-2kii: NMR structure of the SO2144 H-NOX domain from Shewanella oneidens... -

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Basic information

Entry
Database: PDB / ID: 2kii
TitleNMR structure of the 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 / 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 5, 2009Deposition site: BMRB / Processing site: RCSB
Revision 1.0Nov 17, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_conn / 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 / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _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_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)21,1793
Polymers20,5351
Non-polymers6442
Water00
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 the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein Putative uncharacterized protein


Mass: 20534.594 Da / Num. of mol.: 1
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

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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 HN(CA)CB
1513D CBCA(CO)NH
1613D HNHA
1713D HBHA(CO)NH
1813D HN(CA)CO
1913D H(CCO)NH
11013D C(CO)NH
11123D (H)CCH-TOCSY
11223D (H)CCH-COSY
11313D 1H-13C NOESY
11423D 1H-13C NOESY
11533D 1H-15N NOESY
11622D 13C-filtered [F1,F2] NOESY
11722D 1H-1H NOESY
11822D 1H-1H TOCSY
11922D DQF-COSY
12022D 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, K3PO4-1, 90% H2O, 10% D2O90% H2O/10% D2O
20.4-0.8 mM [U-99% 13C; U-99% 15N] H-NOX, DTT, glycerol, K3PO4-2, 100% D2O100% D2O
30.4-0.8 mM [U-99% 15N] H-NOX, DTT, glycerol, K3PO4-3, 90% H2O/10% D2O90% H2O/10% D2O
Sample
UnitsComponentIsotopic labelingConc. range (mg/ml)Solution-ID
mMH-NOX, DTT, glycerol, K3PO4-1[U-99% 13C; U-99% 15N]0.4-0.81
mMH-NOX, DTT, glycerol, K3PO4-2[U-99% 13C; U-99% 15N]0.4-0.82
mMH-NOX, DTT, glycerol, K3PO4-3[U-99% 15N]0.4-0.83
Sample conditionsIonic strength: 50 / pH: 7.4 / Pressure: ambient / Temperature: 308 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: X-PLOR NIH / Developer: Schwieters, C.D. et al. / Classification: refinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR constraintsNOE constraints total: 3262 / NOE intraresidue total count: 941 / NOE long range total count: 717 / NOE medium range total count: 678 / NOE sequential total count: 706
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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