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- PDB-2ms3: The NMR structure of the rubredoxin domain of the NO Reductase Fl... -

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Basic information

Entry
Database: PDB / ID: 2ms3
TitleThe NMR structure of the rubredoxin domain of the NO Reductase Flavorubredoxin from Escherichia coli
ComponentsAnaerobic nitric oxide reductase flavorubredoxin
KeywordsELECTRON TRANSPORT / rubredoxin / flavorubredoxin / nitric oxide reductase / nitric oxide / NorV
Function / homology
Function and homology information


nitric oxide reductase activity / nitric oxide catabolic process / oxidoreductase activity, acting on other nitrogenous compounds as donors / response to nitric oxide / FMN binding / electron transfer activity / iron ion binding / protein-containing complex / identical protein binding / cytoplasm
Similarity search - Function
Anaerobic nitric oxide reductase flavorubredoxin / Rubredoxin-oxygen oxidoreductase / ODP domain / ODP family beta lactamase / Rubrerythrin, domain 2 - #10 / Rubredoxin domain / Rubredoxin / Rubredoxin-like domain / Rubredoxin-like domain profile. / Rubrerythrin, domain 2 ...Anaerobic nitric oxide reductase flavorubredoxin / Rubredoxin-oxygen oxidoreductase / ODP domain / ODP family beta lactamase / Rubrerythrin, domain 2 - #10 / Rubredoxin domain / Rubredoxin / Rubredoxin-like domain / Rubredoxin-like domain profile. / Rubrerythrin, domain 2 / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase / Single Sheet / Flavodoxin / Flavodoxin-like domain profile. / Flavodoxin/nitric oxide synthase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / Flavoprotein-like superfamily / Mainly Beta
Similarity search - Domain/homology
Anaerobic nitric oxide reductase flavorubredoxin
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodSOLUTION NMR / torsion angle dynamics, simulated annealing
Model detailslowest energy, model1
AuthorsTurner, D.L. / Silva, E. / Lamosa, P.M. / Teixeira, M.
CitationJournal: To be Published
Title: The NMR structure of the rubredoxin domain of the NO Reductase Flavorubredoxin from Escherichia coli
Authors: Turner, D.L. / Silva, E. / Lamosa, P.M. / Teixeira, M.
History
DepositionJul 22, 2014Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Jul 22, 2015Provider: repository / Type: Initial release
Revision 1.1May 1, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_conn_angle / 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 / _pdbx_nmr_spectrometer.model / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Anaerobic nitric oxide reductase flavorubredoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,3572
Polymers6,2921
Non-polymers651
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 / 200target function
RepresentativeModel #1lowest energy

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Components

#1: Protein Anaerobic nitric oxide reductase flavorubredoxin / FlRd / FlavoRb


Mass: 6292.064 Da / Num. of mol.: 1 / Fragment: UNP residues 423-479
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria)
Description: The growth medium was enriched with Zn chloride and 15N-labeled ammonium sulfate
Gene: norV, flrD, ygaI, ygaJ, ygaK, b2710, JW2680 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Gold (DE3) / References: UniProt: Q46877
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-1H COSY
1212D 1H-1H TOCSY
1312D 1H-1H NOESY
1412D 1H-15N HSQC
1513D 1H-15N TOCSY

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Sample preparation

DetailsContents: 1.1 mM [U-99% 15N] rubredoxin domain of the NO Reductase Flavorubredoxin-1, 100 mM sodium chloride-2, 10 mM potassium phosphate-3, 0.04 % sodium azide-4, 90 % H2O-5, 10 % D2O-6, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.1 mMrubredoxin domain of the NO Reductase Flavorubredoxin-1[U-99% 15N]1
100 mMsodium chloride-21
10 mMpotassium phosphate-31
0.04 %sodium azide-41
90 %H2O-51
10 %D2O-61
Sample conditionsIonic strength: 0.2 / pH: 7.7 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz

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Processing

NMR software
NameVersionDeveloperClassification
TopSpinBruker Biospincollection
TopSpinBruker Biospinprocessing
Sparky3.111Goddardchemical shift calculation
Sparky3.111Goddarddata analysis
DYANAGuntert, Braun and Wuthrichstructure solution
DYANAGuntert, Braun and Wuthrichrefinement
RefinementMethod: torsion angle dynamics, simulated annealing / Software ordinal: 1
NMR constraintsNOE intraresidue total count: 614 / NOE long range total count: 1197 / NOE medium range total count: 539 / NOE sequential total count: 568
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 200 / Conformers submitted total number: 20 / Maximum lower distance constraint violation: 0.51 Å / Maximum upper distance constraint violation: 0.46 Å / Representative conformer: 1
NMR ensemble rmsDistance rms dev: 0.07 Å

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