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- PDB-2jza: Solution NMR structure of nitrite reductase [NAD(P)H] small subun... -

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Basic information

Entry
Database: PDB / ID: 2jza
TitleSolution NMR structure of nitrite reductase [NAD(P)H] small subunit from Erwinia carotovora. Northeast Structural Genomics Consortium target EwR120
ComponentsNitrite reductase [NAD(P)H] small subunit
KeywordsOXIDOREDUCTASE / ISP domain / Rieske iron-sulfur protein / 3-layer beta-sandwich / Structural Genomics / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG / nirD
Function / homology
Function and homology information


nitrite reductase (NADH) activity / nitrite reductase (NADH) / nitrite reductase complex [NAD(P)H] / nitrate assimilation / 2 iron, 2 sulfur cluster binding / metal ion binding / cytoplasm
Similarity search - Function
Rieske-like [2Fe-2S] domain, NirD-type / Nitrite reductase (NADH) small subunit / NADH-nitrite reductase subunit D family profile. / Rieske-like [2Fe-2S] domain / Rieske Iron-sulfur Protein / Rieske [2Fe-2S] iron-sulphur domain / 3-layer Sandwich / Rieske [2Fe-2S] iron-sulphur domain / Rieske [2Fe-2S] iron-sulfur domain profile. / Rieske [2Fe-2S] iron-sulphur domain superfamily / Mainly Beta
Similarity search - Domain/homology
Nitrite reductase (NADH) small subunit
Similarity search - Component
Biological speciesPectobacterium atrosepticum SCRI1043 (bacteria)
MethodSOLUTION NMR / simulated annealing
AuthorsSathyamoorthy, B. / Eletsky, A. / Wang, D. / Stokes, K. / Owens, L. / Xiao, R. / Liu, J. / Baran, M.C. / Swapna, G.V.T. / Acton, T.B. ...Sathyamoorthy, B. / Eletsky, A. / Wang, D. / Stokes, K. / Owens, L. / Xiao, R. / Liu, J. / Baran, M.C. / Swapna, G.V.T. / Acton, T.B. / Rost, B. / Montelione, G.T. / Szyperski, T. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Solution NMR structure of nitrite reductase [NAD(P)H] small subunit from Erwinia carotovora.
Authors: Sathyamoorthy, B. / Eletsky, A. / Wang, D. / Stokes, K. / Owens, L. / Xiao, R. / Liu, J. / Baran, M.C. / Swapna, G.V.T. / Acton, T.B. / Rost, B. / Montelione, G.T. / Szyperski, T.
History
DepositionDec 31, 2007Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jan 22, 2008Provider: 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_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
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 / _struct_ref_seq_dif.details
Revision 1.3May 29, 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: Nitrite reductase [NAD(P)H] small subunit


Theoretical massNumber of molelcules
Total (without water)14,4801
Polymers14,4801
Non-polymers00
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 / 100target function
RepresentativeModel #1lowest energy

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Components

#1: Protein Nitrite reductase [NAD(P)H] small subunit


Mass: 14480.023 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pectobacterium atrosepticum SCRI1043 (bacteria)
Species: Pectobacterium atrosepticum / Strain: SCRI 1043 / Gene: nirD, ECA4080 / Plasmid: pET21-23C / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+Magic / References: UniProt: Q6CZS1, EC: 1.7.1.4

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1132D 1H-15N HSQC
1233D HNCO
1333D HN(CA)CB
1433D HNCA
1533D CBCA(CO)NH
1623D 1H-15N,13Cali,13Caro NOESY
1722D 1H-15N HSQC
1822D 1H-13C HSQC ali
1923D (H)CCH-COSY aliphatic
11023D (H)CCH-TOCSY aliphatic
11123D HBHA(CO)NH
11222D 1H-13C HSQC aromatic
11322D 1H-13C CT-HSQC aliphatic
11422D 1H-13C CT-HSQC aromatic
11523D (H)CCH-COSY aromatic
11622D 1Haro-15Naro LR-HSQC
11712D 1H-13C CT-HSQC 28ms
11812D 1H-13C CT-HSQC 56ms

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Sample preparation

Details
Solution-IDContentsSolvent system
10.24 mM [U-5% 13C; U-100% 15N] ewr120 protein, 5 mM calcium chloride, 20 mM ammonium acetate, 100 mM sodium chloride, 10 mM DTT, 0.02 % sodium azide, 95% H2O/5% D2O95% H2O/5% D2O
20.7 mM [U-100% 13C; U-100% 15N] ewr120 protein, 5 mM calcium chloride, 20 mM ammonium acetate, 100 mM sodium chloride, 10 mM DTT, 0.02 % sodium azide, 95% H2O/5% D2O95% H2O/5% D2O
30.32 mM [U-100% 13C; U-100% 15N] ewr120 protein, 5 mM calcium chloride, 20 mM ammonium acetate, 100 mM sodium chloride, 10 mM DTT, 0.02 % sodium azide, 95% H2O/5% D2O95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.24 mMewr120 protein[U-5% 13C; U-100% 15N]1
5 mMcalcium chloride1
20 mMammonium acetate1
100 mMsodium chloride1
10 mMDTT1
0.02 %sodium azide1
0.7 mMewr120 protein[U-100% 13C; U-100% 15N]2
5 mMcalcium chloride2
20 mMammonium acetate2
100 mMsodium chloride2
10 mMDTT2
0.02 %sodium azide2
0.32 mMewr120 protein[U-100% 13C; U-100% 15N]3
5 mMcalcium chloride3
20 mMammonium acetate3
100 mMsodium chloride3
10 mMDTT3
0.02 %sodium azide3
Sample conditionsIonic strength: 138 / pH: 5.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE8001
Varian INOVAVarianINOVA7502

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Processing

NMR software
NameVersionDeveloperClassification
AutoStructure2.0.0Huang, Tejero, Powers and Montelionestructure solution
CARA1.8.4Keller and Wuthrichdata analysis
CARA1.8.4Keller and Wuthrichpeak picking
CARA1.8.4Keller and Wuthrichrefinement
CARA1.8.4Keller and Wuthrichchemical shift assignment
CSI2Wishart and Sykesdata analysis
CNS1.2Brunger, Adams, Clore, Gros, Nilges and Readrefinement
MOLMOL2K.2Koradi, Billeter and Wuthrichvisualization
PROSA6.0.2Guntertprocessing
TALOS98.040.21.02Cornilescu, Delaglio and Baxdata analysis
VnmrJ2.1BVariancollection
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
AutoAssign1.15.1Zimmerman, Moseley, Kulikowski and Montelionechemical shift assignment
TopSpin1.4Bruker Biospincollection
TopSpin1.4Bruker Biospinprocessing
RefinementMethod: simulated annealing / Software ordinal: 1 / Details: In explicit water bath
NMR constraintsNOE constraints total: 1000 / NOE intraresidue total count: 266 / NOE long range total count: 349 / NOE medium range total count: 81 / NOE sequential total count: 306 / Protein chi angle constraints total count: 0 / Protein other angle constraints total count: 0 / Protein phi angle constraints total count: 20 / Protein psi angle constraints total count: 20
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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