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- PDB-1dd2: BIOTIN CARBOXYL CARRIER DOMAIN OF TRANSCARBOXYLASE (TC 1.3S) -

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Basic information

Entry
Database: PDB / ID: 1dd2
TitleBIOTIN CARBOXYL CARRIER DOMAIN OF TRANSCARBOXYLASE (TC 1.3S)
ComponentsTRANSCARBOXYLASE 1.3S SUBUNIT
KeywordsTRANSFERASE / ANTIPARALLEL BETA SHEET / HAMMERHEAD / BIOCYTIN
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 HYBRID METHOD
Model type detailsminimized average
AuthorsReddy, D.V. / Shenoy, B.C. / Carey, P.R. / Sonnichsen, F.D.
Citation
Journal: Biochemistry / Year: 2000
Title: High resolution solution structure of the 1.3S subunit of transcarboxylase from Propionibacterium shermanii.
Authors: Reddy, D.V. / Shenoy, B.C. / Carey, P.R. / Sonnichsen, F.D.
#1: Journal: Protein Sci. / Year: 1998
Title: Structural Characterization of the entire 1.3S Subunit of Transcarboxylase from Propionibacterium shermanii
Authors: Reddy, D.V. / Rothemund, S. / Shenoy, B.C. / Carey, P.R. / Sonnichsen, F.D.
#2: Journal: Biochemistry / Year: 1997
Title: Absence of Observable Biotin-Protein Interactions in the 1.3S Subunit of Transcarboxylase: An NMR Study
Authors: Reddy, D.V. / Shenoy, B.C. / Carey, P.R. / Sonnichsen, F.D.
History
DepositionNov 6, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 24, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TRANSCARBOXYLASE 1.3S SUBUNIT


Theoretical massNumber of molelcules
Total (without water)7,8221
Polymers7,8221
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)32 / 50structures with acceptable covalent geometry
RepresentativeModel #1DCZminimized average structure

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Components

#1: Protein TRANSCARBOXYLASE 1.3S SUBUNIT


Mass: 7822.057 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Propionibacterium freudenreichii subsp. shermanii (bacteria)
Species: Propionibacterium freudenreichii / Strain: subsp. shermanii / Production host: Escherichia coli (E. coli) / Strain (production host): HB101
References: UniProt: P02904, methylmalonyl-CoA carboxytransferase

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 13C-SEPARATED NOESY
1213D 15N-SEPARATED NOESY
131HNHA
1424D 13C-SEPARATED NOESY
1533D 15N-SEPARATED NOESY
NMR detailsText: BIOTIN ATTACHED TO LYS 89 WAS OMITTED FROM COORDINATES. RESIDUES 1-46 APPEARED UNSTRUCTURED, OMITTED FROM CALCULATIONS AND COORDINATES.

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Sample preparation

Details
Solution-IDContents
12 MM PROTEIN, N15/C13 LABELED TC 1.3S 1-123, BIOTIN (UNLABELED) COVALENTLY ATTACHED TO LYS 89
22 MM PROTEIN, N15/C13 LABELED TC 1.3S 1-123, BIOTIN (UNLABELED) COVALENTLY ATTACHED TO LYS 89
32MM PROTEIN, N15 LABELED, TC 1.3S 1-123, BIOTIN (UNLABELED) COVALENTLY ATTACHED TO LYS 89
Sample conditionsIonic strength: 0 / pH: 6.7 / Pressure: 1 atm / Temperature: 20 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA6001
Varian INOVAVarianINOVA5002

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipeSGI6X.M4DELAGLIOprocessing
PIPP3.7.3GARRETdata analysis
X-PLOR3.81BRUENGERstructure solution
X-PLOR3.81BRUENGERrefinement
RefinementMethod: DISTANCE GEOMETRY, SIMULATED ANNEALING HYBRID METHOD
Software ordinal: 1
Details: DG_SUB_EMBED, DGSA, REFINE WITH DIRECT J-REFINEMENT
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: structures with acceptable covalent geometry
Conformers calculated total number: 50 / Conformers submitted total number: 32

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