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- PDB-2lzf: Structure of the biofilm matrix promoter AbbA from B. subtilis -

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Basic information

Entry
Database: PDB / ID: 2lzf
TitleStructure of the biofilm matrix promoter AbbA from B. subtilis
ComponentsUncharacterized protein ykzF
KeywordsPROTEIN BINDING / Biofilm / DNA-mimic / AbrB
Function / homologyHelix Hairpins - #3030 / Antirepressor AbbA / Antirepressor AbbA / Helix Hairpins / Orthogonal Bundle / Mainly Alpha / Uncharacterized protein YkzF
Function and homology information
Biological speciesBacillus subtilis (bacteria)
MethodSOLUTION NMR / simulated annealing, molecular dynamics
AuthorsBobay, B.G. / Tucker, A.T. / Losick, R. / Cavanagh, J.
CitationJournal: J.Mol.Biol. / Year: 2014
Title: A DNA Mimic: The Structure and Mechanism of Action for the Anti-Repressor Protein AbbA.
Authors: Tucker, A.T. / Bobay, B.G. / Banse, A.V. / Olson, A.L. / Soderblom, E.J. / Moseley, M.A. / Thompson, R.J. / Varney, K.M. / Losick, R. / Cavanagh, J.
History
DepositionOct 2, 2012Deposition site: BMRB / Processing site: RCSB
Revision 1.0Sep 11, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 19, 2014Group: Database references
Revision 1.2Mar 19, 2014Group: Database references
Revision 1.3Apr 23, 2014Group: Database references
Revision 1.4Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.5May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Uncharacterized protein ykzF
B: Uncharacterized protein ykzF


Theoretical massNumber of molelcules
Total (without water)15,9782
Polymers15,9782
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 / 20structures with the least restraint violations
RepresentativeModel #1lowest energy

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Components

#1: Protein Uncharacterized protein ykzF


Mass: 7989.015 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Strain: 168 / Gene: BSU14120, ykzF / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O31697

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1313D CBCA(CO)NH
1413D C(CO)NH
1513D HNCO
1613D HNCA
1713D HN(CA)CB
1813D HBHA(CO)NH
1913D HN(CO)CA
11013D H(CCO)NH
11123D (H)CCH-TOCSY
11213D HNHA
11313D 1H-15N TOCSY
11413D HN(CA)CO
11513D 1H-15N NOESY
11623D 1H-13C NOESY
11723D 13C-12C isotope filtered NOESY
11812D 1H-15N HSQC RDC
11912D 1H-15N HSQC RDC
NMR detailsText: THE STRUCTURE WAS DETERMINED USING A COMBINATION OF NOE, DIHEDRAL, HYDROGEN BOND AND RESIDUAL DIPOLAR COUPLING DATA.

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Sample preparation

Details
Solution-IDContentsSolvent system
10.5-1.0 mM [U-100% 13C; U-100% 15N] protein, 1 mM DTT, 20 mM TRIS, 200 mM sodium chloride, 1 mM EDTA, 0.02 % sodium azide, 90% H2O/10% D2O90% H2O/10% D2O
20.5-1.0 mM [U-100% 13C; U-100% 15N] protein, 1 mM DTT, 20 mM TRIS, 200 mM sodium chloride, 1 mM EDTA, 0.02 % sodium azide, 100% D2O100% D2O
Sample
Conc. (mg/ml)UnitsComponentIsotopic labelingConc. range (mg/ml)Solution-ID
mMentity-1[U-100% 13C; U-100% 15N]0.5-1.01
1 mMDTT-21
20 mMTRIS-31
200 mMsodium chloride-41
1 mMEDTA-51
0.02 %sodium azide-61
mMentity-7[U-100% 13C; U-100% 15N]0.5-1.02
1 mMDTT-82
20 mMTRIS-92
200 mMsodium chloride-102
1 mMEDTA-112
0.02 %sodium azide-122
Sample conditionsIonic strength: 200 / pH: 6.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE7001
Bruker AvanceBrukerAVANCE9502

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipeVersion 7.5 Rev 2012.204.11.07Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRDrawVersion 7.5 Rev 2012.204.11.07Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRView8aJohnson, One Moon Scientificpeak picking
NMRView8aJohnson, One Moon Scientificdata analysis
NMRView8aJohnson, One Moon Scientificchemical shift assignment
CYANA3Guntert, Mumenthaler and Wuthrichstructure solution
Amber11Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollmanrefinement
RefinementMethod: simulated annealing, molecular dynamics / Software ordinal: 1
Details: 99 INITIAL STRUCTURES WERE CALCULATED WITH CYANA USING NOE, DIHEDRAL, HYDROGEN BOND, AND RDC RESTRAINTS, 99 LOWEST-ENERGY STRUCTURES FROM CYANA WERE REFINED IN AMBER 11 USING THE GB SOLVENT ...Details: 99 INITIAL STRUCTURES WERE CALCULATED WITH CYANA USING NOE, DIHEDRAL, HYDROGEN BOND, AND RDC RESTRAINTS, 99 LOWEST-ENERGY STRUCTURES FROM CYANA WERE REFINED IN AMBER 11 USING THE GB SOLVENT MODEL, 20 LOWEST-ENERGY STRUCTURES WERE DEPOSITED.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 20 / Conformers submitted total number: 20

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