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- PDB-1z6h: Solution Structure of Bacillus subtilis BLAP biotinylated-form -

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Basic information

Entry
Database: PDB / ID: 1z6h
TitleSolution Structure of Bacillus subtilis BLAP biotinylated-form
ComponentsBiotin/Lipoyl Attachment Protein
KeywordsBIOSYNTHETIC PROTEIN / Bacillus subtilis / single-domain Biotin/Lipoyl Attachment Protein / solution structure
Function / homology
Function and homology information


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
Chem-BTI / Biotin/lipoyl attachment protein / Biotin/lipoyl attachment protein
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodSOLUTION NMR / simulated annealing, molecular dynamics
AuthorsCui, G. / Xia, B.
CitationJournal: J.Biol.Chem. / Year: 2006
Title: Identification and solution structures of a single domain biotin/lipoyl attachment protein from Bacillus subtilis
Authors: Cui, G. / Nan, B. / Hu, J. / Wang, Y. / Jin, C. / Xia, B.
History
DepositionMar 22, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 22, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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

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Assembly

Deposited unit
A: Biotin/Lipoyl Attachment Protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,1482
Polymers7,9201
Non-polymers2281
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 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Biotin/Lipoyl Attachment Protein


Mass: 7920.094 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Plasmid: pET 21a(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: Q9R9I3, UniProt: C0H419*PLUS
#2: Chemical ChemComp-BTI / 5-(HEXAHYDRO-2-OXO-1H-THIENO[3,4-D]IMIDAZOL-6-YL)PENTANAL


Mass: 228.311 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N2O2S

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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
1312D NOESY
NMR detailsText: This structure was determined using standard 3D heteronuclear techniques

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Sample preparation

DetailsContents: 1.2mM s-BCCP U-15N,13C; 50mM phosphate buffer NA; 90% H2O, 10% D2O
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 150mM / pH: 7.0 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR3.5Brukercollection
NMRPipe2.1Frank Delaglioprocessing
NMRView5Bruce Johnsondata analysis
CYANA1.0.6Peter Guntertstructure solution
Amber7David Caserefinement
RefinementMethod: simulated annealing, molecular dynamics / Software ordinal: 1
Details: the structures are based on a total of 4560 restraints, 4160 are NOE-derived distance constraints, 117 dihedral angle restraints, 30 distance restraints from hydrogen bonds, 253 charity restraints.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20

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