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- PDB-2p80: Solution structure of the complex between nitrite reductase and p... -

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Basic information

Entry
Database: PDB / ID: 2p80
TitleSolution structure of the complex between nitrite reductase and pseudoazurin from A. faecalis
Components
  • Copper-containing nitrite reductase
  • Pseudoazurin
KeywordsOXIDOREDUCTASE / transient complex / protein-protein interaction / redox partners / electron transfer
Function / homology
Function and homology information


denitrification pathway / nitrite reductase (NO-forming) / nitrite reductase (NO-forming) activity / nitrate assimilation / periplasmic space / electron transfer activity / copper ion binding
Similarity search - Function
Pseudoazurin / Amicyanin/Pseudoazurin / Blue (type 1) copper protein, plastocyanin-type / Nitrite reductase, copper-type / Blue (type 1) copper domain / Copper binding proteins, plastocyanin/azurin family / Blue (type 1) copper protein, binding site / Type-1 copper (blue) proteins signature. / Multicopper oxidase, type 1 / Multicopper oxidase ...Pseudoazurin / Amicyanin/Pseudoazurin / Blue (type 1) copper protein, plastocyanin-type / Nitrite reductase, copper-type / Blue (type 1) copper domain / Copper binding proteins, plastocyanin/azurin family / Blue (type 1) copper protein, binding site / Type-1 copper (blue) proteins signature. / Multicopper oxidase, type 1 / Multicopper oxidase / Multicopper oxidase, N-terminal / Multicopper oxidase / Cupredoxins - blue copper proteins / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / Cupredoxin / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
COPPER (II) ION / GADOLINIUM ATOM / Pseudoazurin / Copper-containing nitrite reductase
Similarity search - Component
Biological speciesAlcaligenes faecalis (bacteria)
MethodSOLUTION NMR / distance geometry, rigid body molecular dynamics, restrained side-chains energy minimization
AuthorsVlasie, M.D. / Ubbink, M.
CitationJournal: To be Published
Title: Low resolution solution structure of the 152 kDa complex between nitrite reductase and pseudoazurin from A. faecalis by paramagnetic NMR.
Authors: Vlasie, M.D. / Fernandez-Busnadiego, R. / Prudencio, M. / Ubbink, M.
History
DepositionMar 21, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 11, 2007Provider: 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_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 / _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: Copper-containing nitrite reductase
B: Copper-containing nitrite reductase
C: Copper-containing nitrite reductase
D: Pseudoazurin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)125,88020
Polymers124,0194
Non-polymers1,86016
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 / 134structures closest to the average
RepresentativeModel #1closest to the average

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Components

#1: Protein Copper-containing nitrite reductase / Cu-NIR


Mass: 36878.648 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Alcaligenes faecalis (bacteria) / Strain: S-6 / Gene: nirK, nir / Plasmid: pET28A / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P38501, nitrite reductase (NO-forming)
#2: Protein Pseudoazurin / Cupredoxin / Blue copper protein


Mass: 13383.511 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Alcaligenes faecalis (bacteria) / Strain: S-6 / Plasmid: pET28A / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P04377
#3: Chemical
ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Cu
#4: Chemical
ChemComp-GD / GADOLINIUM ATOM


Mass: 157.250 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Gd

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experimentType: 2D 15N,1H TROSY
NMR detailsText: ~80% deuteration of the nonexchangeable protons in pseudoazurin

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Sample preparation

Details
Solution-IDContentsSolvent system
1250 mM 15N, 2H pseudoazurin in complex with nitrite reductase -bound GdCLaNP at position 221/223 (0.38 eq), in 50 mM phosphate buffer, H2O, 6% (v/v) D2OH2O, 6% (v/v) D2O
2250 mM 15N, 2H pseudoazurin in complex with nitrite reductase -bound YCLaNP at position 221/223 (0.38 eq), in 50 mM phosphate buffer, H2O, 6% (v/v) D2OH2O, 6% (v/v) D2O
3250 mM 15N, 2H pseudoazurin in complex with nitrite reductase -bound GdCLaNP at position 234/236 (0.32 eq), in 50 mM phosphate buffer, H2O, 6% (v/v) D2OH2O, 6% (v/v) D2O
4250 mM 15N, 2H pseudoazurin in complex with nitrite reductase -bound YCLaNP at position 234/236 (0.32 eq), in 50 mM phosphate buffer, H2O, 6% (v/v) D2OH2O, 6% (v/v) D2O
5250 mM 15N, 2H pseudoazurin in complex with nitrite reductase -bound GdCLaNP at position 333/336 (0.53 eq), in 50 mM phosphate buffer, H2O, 6% (v/v) D2OH2O, 6% (v/v) D2O
6250 mM 15N, 2H pseudoazurin in complex with nitrite reductase -bound YCLaNP at position 333/336 (0.53 eq), in 50 mM phosphate buffer, H2O, 6% (v/v) D2OH2O, 6% (v/v) D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
150 mM phosphate 6.51 atm298 K
250 mM phosphate 6.51 atm298 K
350 mM phosphate 6.51 atm298 K
450 mM phosphate 6.51 atm298 K
550 mM phosphate 6.51 atm298 K
650 mM phosphate 6.51 atm298 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Bruker DMX / Manufacturer: Bruker / Model: DMX / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2.6Brukercollection
Azara2.7Boucher, W.processing
ANSIG1.02Kraulis, P.data analysis
X-PLOR2.9.9Brunger, A.T. et al.structure solution
MestReC4.8.6.0Mestrelab Researchdata analysis
X-PLOR2.9.9Brunger, A.T. et al.refinement
RefinementMethod: distance geometry, rigid body molecular dynamics, restrained side-chains energy minimization
Software ordinal: 1
Details: 324 distance restraints from paramagnetic relaxation, 5 restraints from chemical shift perturbations
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures closest to the average
Conformers calculated total number: 134 / Conformers submitted total number: 20

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