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- PDB-6wqe: Solution Structure of the IWP-051-bound H-NOX from Shewanella woo... -

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Basic information

Entry
Database: PDB / ID: 6wqe
TitleSolution Structure of the IWP-051-bound H-NOX from Shewanella woodyi in the Fe(II)CO ligation state
ComponentsHeme NO binding domain protein
KeywordsSIGNALING PROTEIN / hemoprotein / nitric oxide / signaling / sGC stimulator Complex
Function / homologyHeme NO-binding / H-NOX domain superfamily / Haem-NO-binding / NO signalling/Golgi transport ligand-binding domain superfamily / heme binding / CARBON MONOXIDE / PROTOPORPHYRIN IX CONTAINING FE / Chem-IWP / Heme NO binding domain protein
Function and homology information
Biological speciesShewanella woodyi (bacteria)
MethodSOLUTION NMR / simulated annealing
AuthorsChen, C.Y. / Lee, W. / Montfort, W.R.
Funding support United States, 4items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM117357 United States
American Heart Association17POST33670593 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P41 GM103399 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P41GM66326 United States
CitationJournal: Protein Sci. / Year: 2021
Title: Solution structures of the Shewanella woodyi H-NOX protein in the presence and absence of soluble guanylyl cyclase stimulator IWP-051.
Authors: Chen, C.Y. / Lee, W. / Renhowe, P.A. / Jung, J. / Montfort, W.R.
History
DepositionApr 28, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 22, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 9, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Mar 3, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.3May 1, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Heme NO binding domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,7674
Polymers21,7681
Non-polymers1,0003
Water0
1


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

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Components

#1: Protein Heme NO binding domain protein


Mass: 21767.539 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shewanella woodyi (bacteria) / Production host: Escherichia coli (E. coli) / Strain (production host): Tuner pLysS / References: UniProt: B1KIH6
#2: Chemical ChemComp-IWP / 5-fluoro-2-{1-[(2-fluorophenyl)methyl]-5-(1,2-oxazol-3-yl)-1H-pyrazol-3-yl}pyrimidin-4-ol


Mass: 355.298 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H11F2N5O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


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


Mass: 28.010 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CO
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N HSQC
121isotropic22D 1H-15N TROSY
231anisotropic22D 1H-15N TROSY
142isotropic12D 13C15Nfiltered NOESY
3104isotropic42D 1H-1H NOESY
192isotropic12D 1H-13C HSQC aliphatic
153isotropic22D 1H-13C HSQC
161isotropic13D 1H-15N NOESY
172isotropic13D 1H-13C NOESY aliphatic
183isotropic33D 1H-13C NOESY aliphatic

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Sample preparation

Details
TypeSolution-IDContentsDetailsLabelSolvent system
solution1500 uM [U-99% 15N] Protein, 2400 uM ligand, 90% H2O/10% D2O15N labeled H-NOX protein (500 uM) + unlabeled (IWP051 2400 uM)15N_sample_IWP05190% H2O/10% D2O
solution2600 uM [U-99% 13C; U-99% 15N] protein, 3500 uM ligand, 100% D2O13C15N labeled H-NOX protein (600 uM) + unlabeled IWP051 (3500 uM) in 99.9% D2O13C15N_D2O_sample_IWP051100% D2O
solution3600 uM [U-99% 15N] protein, 3000 uM 13C labeled on the benzene carbon ligand, 100% D2O13C labeled IWP051 (3000 uM) + 15N labeled H-NOX (600 uM) in 99.9% D2O13C_IWP051_protein100% D2O
solution415.0 uM protein, 292.0 uM ligand, 100% D2Ounlabeled IWP-051 (292 uM) bound to Sw H-NOX (15 uM) in D2OIWP051_protein_TrNOESY100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
500 uMProtein[U-99% 15N]1
2400 uMligandnone1
600 uMprotein[U-99% 13C; U-99% 15N]2
3500 uMligandnone2
600 uMprotein[U-99% 15N]3
3000 uMligand13C labeled on the benzene carbon3
15.0 uMproteinnone4
292.0 uMligandnone4
Sample conditions

Ionic strength err: 0.2 / pH: 7.4 / PH err: 0.05 / Pressure: 1 atm / Pressure err: 0.01 / Temperature err: 0.2

Conditions-IDDetailsIonic strengthLabelTemperature (K)
150 mM sodium/potassium phosphate (pH 7.4), 50 mM NaCl50 mMconditions_1293 K
250 mM sodium/potassium phosphate (pH 7.4), 50 mM NaCl 15 mg/mL pf1 phage50 mMconditions_2293 K
350 mM sodium phosphate (pH 7.5), 100 mM NaCl, 4% DMSO-d6, 2 mM dithionite and 100 uM DSS100 mMconditions_3298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-IDDetails
Agilent agilent 800Agilentagilent 80080015 mm z-axis pulsed field gradient triple resonance Cold probe
Agilent agilent 600Agilentagilent 60060045 mm z-axis pulsed field gradient triple resonance Cold probe
Bruker AVANCE NEOBrukerAVANCE NEO60025 mm z-axis pulsed field gradient triple resonance Cold probe
Bruker AVANCE NEOBrukerAVANCE NEO80035 mm z-axis pulsed field gradient triple resonance Cold probe

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Processing

NMR software
NameDeveloperClassification
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure calculation
SparkySparky: Goddard NMRFAM-Sparky: Lee W, Tonelli M, Markley JLchemical shift assignment
SparkySparky: Goddard NMRFAM-Sparky: Lee W, Tonelli M, Markley JLpeak picking
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
VNMRVariancollection
TopSpinBruker Biospincollection
RefinementMethod: simulated annealing / Software ordinal: 1
Details: distance geometry,torsion angle dynamics,molecular dynamics
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with acceptable covalent geometry
Conformers calculated total number: 200 / Conformers submitted total number: 20

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