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- PDB-1o78: Biotin carboxyl carrier domain of transcarboxylase (1.3S) [10-48]... -

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Basic information

Entry
Database: PDB / ID: 1o78
TitleBiotin carboxyl carrier domain of transcarboxylase (1.3S) [10-48] deletion mutant
ComponentsBIOTIN CARBOXYL CARRIER PROTEIN OF METHYLMALONYL-COA CARBOXYL-TRANSFERASE
KeywordsCARRIER PROTEIN / TRANSCARBOXYLASE / CARBOXYL CARRIER / TRANSFERASE
Function / homology
Function and homology information


methylmalonyl-CoA carboxytransferase / methylmalonyl-CoA carboxytransferase activity
Similarity search - Function
: / 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
Methylmalonyl-CoA carboxyltransferase 1.3S subunit
Similarity search - Component
Biological speciesPROPIONIBACTERIUM FREUDENREICHII SUBSP. SHERMANII (bacteria)
MethodSOLUTION NMR / DISTANCE GEOMETRY, SIMULATED ANNEALING
AuthorsJank, M.M. / Sadowsky, J.D. / Peikert, C. / Berger, S.
Citation
Journal: Int.J.Biol.Macromol. / Year: 2002
Title: NMR Studies on the Solution Structure of a Deletion Mutant of the Transcarboxylase Biotin Carrier Subunit
Authors: Jank, M.M. / Sadowsky, J.D. / Peikert, C. / Berger, S.
#1: Journal: Biochemistry / Year: 2000
Title: High Resolution Solution Structure of the 1.3S Subunit of Transcarboxylase from Propionibacterium Shermanii(Dagger)
Authors: Reddy, D.V. / Shenoy, B.C. / Carey, P.R. / Sonnichsen, F.D.
#2: Journal: Protein Expr.Purif. / Year: 1999
Title: Expression and Biotinylation of a Mutant of the Transcarboxylase Carrier Protein from Propioni Shermanii
Authors: Jank, M.M. / Bokorny, S. / Roehm, K.-H. / Berger, S.
History
DepositionOct 24, 2002Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 21, 2002Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 15, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_nmr_software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_mr / _pdbx_nmr_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: BIOTIN CARBOXYL CARRIER PROTEIN OF METHYLMALONYL-COA CARBOXYL-TRANSFERASE


Theoretical massNumber of molelcules
Total (without water)8,6671
Polymers8,6671
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 / 600LEAST RESTRAINT VIOLATION
RepresentativeModel #3

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Components

#1: Protein BIOTIN CARBOXYL CARRIER PROTEIN OF METHYLMALONYL-COA CARBOXYL-TRANSFERASE / TRANSCARBOXYLASE / 1.3S SUBUNIT


Mass: 8667.160 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: RESIDUES 10-48 DELETION MUTANT
Source: (gene. exp.) PROPIONIBACTERIUM FREUDENREICHII SUBSP. SHERMANII (bacteria)
Plasmid: PTAC1.3DELTA10-48, PCY216 / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P02904
Compound detailsBIOTINYL 1.3S SUBUNIT (CHAIN A) SERVES AS A CARBOXYL CARRIER BETWEEN THE SUBSTRATE BINDING SITES ON ...BIOTINYL 1.3S SUBUNIT (CHAIN A) SERVES AS A CARBOXYL CARRIER BETWEEN THE SUBSTRATE BINDING SITES ON THE 12S AND 5S SUBUNITS. TRANSCARBOXYLASE IS COMPRISED OF THREE SUBUNITS: 1.3S, 5S, AND 12S. RESIDUES 10-48 DELETION MUTANT, CHAIN A
Sequence detailsRESIDUES 10-48 DELETION MUTANT

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
11115N-HSQC-NOESY
121HNCA
131HNCO
141CBCANH
151CBCA(CO)NH
161HN(CA)CO
171HCACO
181HN-HSQC-TOCSY
191HBHA(CBCACO)NH
1101(H)N(CA)NNH
1111(H)CCH-TOCSY
11212D 15N-1H HSQC
NMR detailsText: THE STRUCTURE WAS DETERMINED USING TRIPLE-RESONANCE NMR SPECTROSCOPY ON 13C, 15N-LABELED PROTEIN. BIOTIN WAS UNLABELED AND NOT INCLUDED IN THE STRUCTURE CALCULATION.

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Sample preparation

DetailsContents: 2.3 MM PROTEIN, N15/C13 LABELED TC 1.3S [10-48], BIOTIN (UNLABELED) COVALENTLY ATTACHED TO LYS 89
Sample conditionsIonic strength: 2 MM AMMONIUM ACETATE / pH: 4.5 / Pressure: 1 atm / Temperature: 300 K
Crystal grow
*PLUS
Method: other / Details: NMR

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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
NameVersionDeveloperClassification
X-PLOR3.1BRUNGERrefinement
X-PLORstructure solution
PROCHECK / PROCHECK-NMR3.5.3structure solution
AQUA2structure solution
RefinementMethod: DISTANCE GEOMETRY, SIMULATED ANNEALING / Software ordinal: 1
Details: DGSA, REFINEMENT WITH NOES AND HYDROGEN-BOND CONSTRAINTS
NMR ensembleConformer selection criteria: LEAST RESTRAINT VIOLATION / Conformers calculated total number: 600 / Conformers submitted total number: 20

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