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- PDB-2lju: Solution structure of putative oxidoreductase from Ehrlichia chaf... -

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Basic information

Entry
Database: PDB / ID: 2lju
TitleSolution structure of putative oxidoreductase from Ehrlichia chaffeensis, Seattle Structural Genomics Center for Infectious Disease (SSGCID)
ComponentsPutative oxidoreductase
KeywordsOXIDOREDUCTASE / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID
Function / homology
Function and homology information


oxidoreductase activity, acting on NAD(P)H / : / electron transport chain
Similarity search - Function
atu1810 like domain / NADH dehydrogenase ubiquinone Fe-S protein 4-like superfamily / NADH dehydrogenase ubiquinone Fe-S protein 4 / NADH dehydrogenase ubiquinone Fe-S protein 4, mitochondrial / Double Stranded RNA Binding Domain / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Putative oxidoreductase
Similarity search - Component
Biological speciesEhrlichia chaffeensis (bacteria)
MethodSOLUTION NMR / torsion angle dynamics
Model detailsfewest violations, model 1
AuthorsYang, F. / Barnwal, R. / Varani, G. / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: To be Published
Title: Solution structure of putative oxidoreductase from Ehrlichia chaffeensis
Authors: Yang, F. / Barnwal, R. / Varani, G.
History
DepositionSep 29, 2011Deposition site: BMRB / Processing site: RCSB
Revision 1.0Oct 19, 2011Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
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: Putative oxidoreductase


Theoretical massNumber of molelcules
Total (without water)12,3141
Polymers12,3141
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 #1fewest violations

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Components

#1: Protein Putative oxidoreductase


Mass: 12313.978 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ehrlichia chaffeensis (bacteria) / Strain: Arkansas / Gene: ECH_0213 / Production host: Escherichia coli (E. coli) / References: UniProt: Q2GHP7

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1222D 1H-13C HSQC
1312D 1H-1H NOESY
1423D CBCA(CO)NH
1523D HNCO
1623D HNCA
1723D HN(CA)CB
1823D HBHA(CO)NH
1923D (H)CCH-TOCSY
11023D 1H-15N NOESY
11123D 1H-13C NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.5 mM [U-95% 15N] protein, 20 mM potassium phosphate, 100 mM sodium chloride, 1 mM DTT, 90% H2O/10% D2O90% H2O/10% D2O
20.5 mM [U-95% 13C; U-95% 15N] protein, 20 mM potassium phosphate, 100 mM sodium chloride, 1 mM DTT, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMentity-1[U-95% 15N]1
20 mMpotassium phosphate-21
100 mMsodium chloride-31
1 mMDTT-41
0.5 mMentity-5[U-95% 13C; U-95% 15N]2
20 mMpotassium phosphate-62
100 mMsodium chloride-72
1 mMDTT-82
Sample conditionspH: 7.0 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AMXBrukerAMX5001
Bruker AvanceBrukerAVANCE6002

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Processing

NMR software
NameDeveloperClassification
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
MOLMOLKoradi, Billeter and Wuthrichstructure display
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
TopSpinBruker Biospincollection
TALOSCornilescu, Delaglio and Baxdata analysis
CcpNMRCCPNchemical shift assignment
CYANAGuntert, Mumenthaler and Wuthrichrefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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