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- PDB-3bdo: SOLUTION STRUCTURE OF APO-BIOTINYL DOMAIN FROM ACETYL COENZYME A ... -

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Basic information

Entry
Database: PDB / ID: 3bdo
TitleSOLUTION STRUCTURE OF APO-BIOTINYL DOMAIN FROM ACETYL COENZYME A CARBOXYLASE OF ESCHERICHIA COLI DETERMINED BY TRIPLE-RESONANCE NMR SPECTROSCOPY
ComponentsPROTEIN (ACETYL-COA CARBOXYLASE)
KeywordsBIOTIN / BIOTINYL DOMAIN / ACETYL COA CARBOXYLASE / SWINGING ARM / NMR SPECTROSCOPY / PROTEIN STRUCTURE
Function / homology
Function and homology information


acetyl-CoA carboxylase complex / malonyl-CoA biosynthetic process / acetyl-CoA carboxylase activity / fatty acid biosynthetic process / molecular adaptor activity / cytosol / cytoplasm
Similarity search - Function
Acetyl-CoA biotin carboxyl carrier / Biotin-binding site / Biotin-requiring enzymes attachment site. / RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain / Biotin-requiring enzyme / Biotinyl/lipoyl domain profile. / Biotin/lipoyl attachment / Single hybrid motif / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Biotin carboxyl carrier protein of acetyl-CoA carboxylase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodSOLUTION NMR
AuthorsRoberts, E.L. / Shu, N. / Howard, M.J. / Broadhurst, R.W. / Chapman-Smith, A. / Wallace, J.C. / Morris, T. / Cronan, J.E. / Perham, R.N.
CitationJournal: Biochemistry / Year: 1999
Title: Solution structures of apo and holo biotinyl domains from acetyl coenzyme A carboxylase of Escherichia coli determined by triple-resonance nuclear magnetic resonance spectroscopy.
Authors: Roberts, E.L. / Shu, N. / Howard, M.J. / Broadhurst, R.W. / Chapman-Smith, A. / Wallace, J.C. / Morris, T. / Cronan Jr., J.E. / Perham, R.N.
History
DepositionMar 8, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0Apr 26, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROTEIN (ACETYL-COA CARBOXYLASE)


Theoretical massNumber of molelcules
Total (without water)8,8421
Polymers8,8421
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 40LOWEST ENERGY
RepresentativeModel #1

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Components

#1: Protein PROTEIN (ACETYL-COA CARBOXYLASE) / HOLO BIOTINYL DOMAIN


Mass: 8842.172 Da / Num. of mol.: 1 / Fragment: BIOTINYL DOMAIN, RESIDUES 77 - 156
Source method: isolated from a genetically manipulated source
Details: BIOTINYL DOMAIN MADE BY EXPRESSING BIOTIN DOMAIN SUBGENE IN A STRAIN IN WHICH BIOTIN PROTEIN LIGASE IS ALSO EXPRESSED, LEADING TO PARTIAL BIOTINYLATION IN VIVO
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: BL21(DE3) / Plasmid: PTM53 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P0ABD8, acetyl-CoA carboxylase

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111DQF-COSY
121NOESY
13115N-1H-HSQC
141HNHA
151HNHB
16115N-NOESY-HMQC
17115N-TOCSY-HMQC
181HN(CA)CB
19113C-NOESY-HSQC
1101(H)CCH-TOCSY
NMR detailsText: THE STRUCTURE WAS DETERMINED USING TRIPLE-RESONANCE NMR SPECTROSCOPY ON 13C, 15N-LABELED PROTEIN

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Sample preparation

DetailsContents: 90% WATER/10% D2O
Sample conditionsIonic strength: 20mM SODIUM PHOSPHATE / pH: 6.8 / Pressure: 1 atm / Temperature: 303 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AM500BrukerAM5005001
Bruker AMX600BrukerAMX6006002

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR3.1BRUNGERrefinement
Azarastructure solution
ANSIGstructure solution
XPLORstructure solution
RefinementSoftware ordinal: 1
Details: REFINEMENT DETAILS CAN BE FOUND IN THE JRNL CITATION ABOVE.
NMR ensembleConformer selection criteria: LOWEST ENERGY / Conformers calculated total number: 40 / Conformers submitted total number: 20

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