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- PDB-2lxr: Solution structure of HP1264 from Helicobacter pylori -

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Basic information

Entry
Database: PDB / ID: 2lxr
TitleSolution structure of HP1264 from Helicobacter pylori
ComponentsNADH dehydrogenase I subunit E
KeywordsOXIDOREDUCTASE / HP1264
Function / homologyPutative NADH-ubiquinone oxidoreductase chain E / putative NADH-ubiquinone oxidoreductase chain E / TusA-like domain / TusA-like domain superfamily / Translation Initiation Factor IF3 / 2-Layer Sandwich / Alpha Beta / NADH-ubiquinone oxidoreductase chain E
Function and homology information
Biological speciesHelicobacter pylori (bacteria)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model1
AuthorsLee, K.
CitationJournal: To be Published
Title: Solution structure of HP1264, Complex I subunit E from Helicobacter pylori, reveals a novel fold for FMN binding protein
Authors: Lee, K.
History
DepositionAug 31, 2012Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Oct 3, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 1.2May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NADH dehydrogenase I subunit E


Theoretical massNumber of molelcules
Total (without water)8,9391
Polymers8,9391
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 / 20structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein NADH dehydrogenase I subunit E


Mass: 8939.365 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (bacteria) / Strain: ATCC 700392 / 26695 / Gene: HP_1264 / Production host: Escherichia coli (E. coli) / References: UniProt: O25854

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D CBCA(CO)NH
1313D C(CO)NH
1413D HNCO
1513D HNCA
1613D HN(CA)CB
1713D HBHA(CO)NH
1813D HN(CO)CA
1913D H(CCO)NH
11013D 1H-15N NOESY
11113D 1H-13C NOESY
11213D (H)CCH-TOCSY
11313D HN(CA)CO

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Sample preparation

DetailsContents: 1 mM [U-100% 13C; U-100% 15N] sodium phosphate-1, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
SampleConc.: 1 mM / Component: sodium phosphate-1 / Isotopic labeling: [U-100% 13C; U-100% 15N]
Sample conditionsIonic strength: 0.15 / pH: 6 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 600 MHz

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Processing

NMR software
NameDeveloperClassification
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
CYANArefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 20 / Conformers submitted total number: 20 / Representative conformer: 1

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