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- PDB-2jo6: NMR structure of the E.coli protein NirD, Northeast Structural Ge... -

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Basic information

Entry
Database: PDB / ID: 2jo6
TitleNMR structure of the E.coli protein NirD, Northeast Structural Genomics target ET100
ComponentsNitrite reductase [NAD(P)H] small subunit
KeywordsOXIDOREDUCTASE / all beta / ISP domain / Rieske iron-sulfur protein / 3-layer sandwich / Structural Genomics / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homology
Function and homology information


nitrite reductase (NADH) / nitrite reductase [NAD(P)H] activity / nitrite reductase complex [NAD(P)H] / anaerobic respiration / nitrate assimilation / 2 iron, 2 sulfur cluster binding / cytoplasm
Similarity search - Function
NADH-nitrite reductase subunit D family profile. / Rieske-like [2Fe-2S] domain, NirD-type / Nitrite reductase (NADH) small subunit / Rieske-like [2Fe-2S] domain / Rieske Iron-sulfur Protein / Rieske [2Fe-2S] iron-sulphur domain / 3-layer Sandwich / Rieske [2Fe-2S] iron-sulphur domain superfamily / Mainly Beta
Similarity search - Domain/homology
Nitrite reductase (NADH) small subunit
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodSOLUTION NMR / simulated annealing
Model detailsnitrite reductase small subunit.
AuthorsRamelot, T.A. / Cort, J.R. / Yee, A.A. / Guido, V. / Lukin, J.A. / Arrowsmith, C.H. / Kennedy, M.A. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: NMR structure of E.coli NirD.
Authors: Ramelot, T.A. / Cort, J.R. / Yee, A.A. / Arrowsmith, C.H. / Kennedy, M.A.
History
DepositionFeb 21, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 27, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 5, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Experimental preparation / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_sample_details / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_sample_details.contents ..._pdbx_database_status.status_code_cs / _pdbx_nmr_sample_details.contents / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
Revision 1.4Dec 20, 2023Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.deposit_site
Revision 1.5May 8, 2024Group: Database references / Category: database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: Nitrite reductase [NAD(P)H] small subunit


Theoretical massNumber of molelcules
Total (without water)12,7661
Polymers12,7661
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 25structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

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


Mass: 12766.440 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: nirD / Production host: Escherichia coli (E. coli) / References: UniProt: P0A9I8, nitrite reductase [NAD(P)H]

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR / Details: nitrite reductase small subunit
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 1H-15N NOESY
1212D 1H-15N HSQC
1312D 1H-13C HSQC
1413D HN(CA)CB
1513D 1H-13C NOESY
1624D CC NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
11 mM [U-100% 13C] protein, 10 mM TRIS, 300 mM sodium chloride, 10 uM ZINC ION, 10 mM DTT, 0.01 % sodium azide, 95% H2O/5% D2O95% H2O/5% D2O
21 mM [U-100% 13C] protein, 10 mM TRIS, 300 mM sodium chloride, 10 uM ZINC ION, 10 mM DTT, 0.01 % sodium azide, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMprotein[U-100% 13C]1
10 mMTRIS1
300 mMsodium chloride1
10 uMZINC ION1
10 mMDTT1
0.01 %sodium azide1
1 mMprotein[U-100% 13C]2
10 mMTRIS2
300 mMsodium chloride2
10 uMZINC ION2
10 mMDTT2
0.01 %sodium azide2
Sample conditionsIonic strength: 300 / pH: 7.0 / Pressure: ambient / Temperature: 293 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA6001
Varian INOVAVarianINOVA7502

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Processing

NMR software
NameVersionDeveloperClassification
AutoStructure2.1.1Huang, Swapana, Rajan, Ke, Xia, Shukla, Inouye and Montelionedata analysis
X-PLOR NIH2.15.0Schwieters, Kuszewski, Tjandra and Clorestructure solution
CNS1.1Brunger, Adams, Clore, Gros, Nilges and Readrefinement
Sparky3.1Goddardpeak picking
NMRPipelinux9Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
RefinementMethod: simulated annealing / Software ordinal: 1
Details: simulated annealing using NIH xplor, followed by cns water refinement.
NMR constraintsNOE constraints total: 912 / NOE intraresidue total count: 0 / NOE long range total count: 643 / NOE medium range total count: 170 / NOE sequential total count: 99
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 25 / Conformers submitted total number: 20 / Maximum lower distance constraint violation: -0.03 Å / Maximum upper distance constraint violation: 0.02 Å
NMR ensemble rmsDistance rms dev: 0.001 Å / Distance rms dev error: 0.0001 Å

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