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- PDB-2bru: Complex of the domain I and domain III of Escherichia coli transh... -

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Basic information

Entry
Database: PDB / ID: 2bru
TitleComplex of the domain I and domain III of Escherichia coli transhydrogenase
Components
  • NAD(P) TRANSHYDROGENASE SUBUNIT ALPHA
  • NAD(P) TRANSHYDROGENASE SUBUNIT BETA
KeywordsOXIDOREDUCTASE / PARAMAGNETIC NMR / TRANSHYDROGENASE / INNER MEMBRANE / MEMBRANE / NAD / NADP / TRANSMEMBRANE
Function / homology
Function and homology information


proton export across plasma membrane / proton-translocating NAD(P)+ transhydrogenase activity / proton-translocating NAD(P)+ transhydrogenase / NADPH regeneration / membrane => GO:0016020 / NADP binding / oxidoreductase activity / protein dimerization activity / plasma membrane
Similarity search - Function
NAD(P) transhydrogenase, alpha subunit / NAD(P) transhydrogenase, alpha subunit, C-terminal / 4TM region of pyridine nucleotide transhydrogenase, mitoch / NADP transhydrogenase, beta subunit / NADP transhydrogenase beta-like domain / NAD(P) transhydrogenase beta subunit / Alanine dehydrogenase/NAD(P) transhydrogenase, conserved site-1 / Alanine dehydrogenase & pyridine nucleotide transhydrogenase signature 1. / Alanine dehydrogenase/pyridine nucleotide transhydrogenase, conserved site-2 / Alanine dehydrogenase & pyridine nucleotide transhydrogenase signature 2. ...NAD(P) transhydrogenase, alpha subunit / NAD(P) transhydrogenase, alpha subunit, C-terminal / 4TM region of pyridine nucleotide transhydrogenase, mitoch / NADP transhydrogenase, beta subunit / NADP transhydrogenase beta-like domain / NAD(P) transhydrogenase beta subunit / Alanine dehydrogenase/NAD(P) transhydrogenase, conserved site-1 / Alanine dehydrogenase & pyridine nucleotide transhydrogenase signature 1. / Alanine dehydrogenase/pyridine nucleotide transhydrogenase, conserved site-2 / Alanine dehydrogenase & pyridine nucleotide transhydrogenase signature 2. / Alanine dehydrogenase/pyridine nucleotide transhydrogenase, N-terminal / Alanine dehydrogenase/PNT, C-terminal domain / Alanine dehydrogenase/PNT, N-terminal domain / Alanine dehydrogenase/PNT, C-terminal domain / Alanine dehydrogenase/PNT, N-terminal domain / Alanine dehydrogenase/pyridine nucleotide transhydrogenase, NAD(H)-binding domain / TPP-binding domain / DHS-like NAD/FAD-binding domain superfamily / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / NAD(P) transhydrogenase subunit alpha / NAD(P) transhydrogenase subunit beta / NAD(P) transhydrogenase subunit beta
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodSOLUTION NMR / RIGID BODY MINIMIZATION, MOLECULAR DYNAMICS SIMULATION
AuthorsJohansson, T. / Pedersen, A. / Leckner, J. / Karlsson, B.G.
CitationJournal: To be Published
Title: Structure Determination of a Transient Complex by NMR Using Paramagnetic Distance Restraints - the Complex of the Soluble Domains of Escherichia Coli Transhydrogenase
Authors: Johansson, T. / Pedersen, A. / Leckner, J. / Karlsson, B.G.
History
DepositionMay 11, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 29, 2006Provider: repository / Type: Initial release
Revision 1.1May 15, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NAD(P) TRANSHYDROGENASE SUBUNIT ALPHA
B: NAD(P) TRANSHYDROGENASE SUBUNIT ALPHA
C: NAD(P) TRANSHYDROGENASE SUBUNIT BETA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,5545
Polymers106,1473
Non-polymers1,4072
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 10
RepresentativeModel #1

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Components

#1: Protein NAD(P) TRANSHYDROGENASE SUBUNIT ALPHA / PYRIDINE NUCLEOTIDE TRANSHYDROGENASE SUBUNIT ALPHA / NICOTINAMIDE NUCLEOTIDE TRANSHYDROGENASE SUBUNIT ALPHA


Mass: 42863.883 Da / Num. of mol.: 2 / Fragment: DOMAIN I, RESIDUES 2-394
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): JM109 / References: UniProt: P07001, EC: 1.6.1.2
#2: Protein NAD(P) TRANSHYDROGENASE SUBUNIT BETA / PYRIDINE NUCLEOTIDE TRANSHYDROGENASE SUBUNIT BETA / NICOTINAMIDE NUCLEOTIDE TRANSHYDROGENASE SUBUNIT BETA


Mass: 20419.172 Da / Num. of mol.: 1 / Fragment: DOMAIN III, RESIDUES 286-462
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P07002, UniProt: P0AB67*PLUS, EC: 1.6.1.2
#3: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#4: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H28N7O17P3
Compound detailsFUNCTION: PROTON PUMP ACROSS THE MEMBRANE
Sequence detailsALL CHAINS INCLUDE N-TERMINAL HIS-TAGS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experimentType: HSQC
NMR detailsText: NONE

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Sample preparation

DetailsContents: 95% H2O/5% D2O
Sample conditionsIonic strength: 110 mM / pH: 7 / Pressure: 1.0 atm / Temperature: 298.0 K

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NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 800 MHz

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Processing

NMR software
NameDeveloperClassification
X-PLORBRUNGERrefinement
X-PLORstructure solution
RefinementMethod: RIGID BODY MINIMIZATION, MOLECULAR DYNAMICS SIMULATION
Software ordinal: 1
Details: REFINEMENT DETAILS CAN BE FOUND IN THE JRNL CITATION ABOVE
NMR ensembleConformers calculated total number: 10 / Conformers submitted total number: 10

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