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- PDB-2k6l: The solution structure of XACb0070 from Xanthonomas axonopodis pv... -

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Basic information

Entry
Database: PDB / ID: 2k6l
TitleThe solution structure of XACb0070 from Xanthonomas axonopodis pv citri reveals this new protein is a member of the RHH family of transcriptional repressors
ComponentsPutative uncharacterized protein
KeywordsUNKNOWN FUNCTION / Xanthonomas axonopodis / RHH / structural proteomics / Plasmid / Hypothetical DNA binding protein
Function / homologyXACb0070, ribbon-helix-helix domain / Ribbon-helix-helix domain / Met repressor-like / Arc Repressor Mutant / Arc-type ribbon-helix-helix / regulation of DNA-templated transcription / Orthogonal Bundle / Mainly Alpha / RHH_6 domain-containing protein
Function and homology information
Biological speciesXanthomonas axonopodis pv. citri (bacteria)
MethodSOLUTION NMR / simulated annealing
Model detailsThis entry consists in the structure of the hydrophobic core of XACb0070 (residues 1-51)
AuthorsGallo, M. / Cicero, D.O. / Amata, I. / Eliseo, T. / Paci, M. / Spisni, A. / Ferrari, E. / Pertinhez, T.A. / Farah, C.S.
CitationJournal: To be Published
Title: The solution structure reveals that XACb0070 from the plant pathogen Xanthomonas citri belongs to the RHH superfamily of bacterial DNA-binding proteins
Authors: Gallo, M. / Ferrari, E. / Amata, I. / Eliseo, T. / Pertinhez, T.A. / Paci, M. / Farah, C.S. / Spisni, A. / Cicero, D.O.
History
DepositionJul 11, 2008Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Jun 16, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 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
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
Revision 1.3May 29, 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: Putative uncharacterized protein
B: Putative uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)11,5012
Polymers11,5012
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 / 500structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Putative uncharacterized protein


Mass: 5750.508 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: XACb0070 exists as a homodimer in solution.
Source: (gene. exp.) Xanthomonas axonopodis pv. citri (bacteria)
Gene: XACa0037, XACb0070 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / Variant (production host): (DE3)pLysS / References: UniProt: Q8NL33

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
Details: This entry consists in the structure of the hydrophobic core of XACb0070 (residues 1-51)
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
2222D 1H-15N HSQC
2332D 1H-13C HSQC
1412D 1H-1H TOCSY
1512D 1H-1H NOESY
2623D CBCA(CO)NH
2723D HNCO
2823D HNCA
2923D HBHA(CO)NH
21032D 1H-1H NOESY
2112HetNOE
2122T1
2132T2

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Sample preparation

Details
Solution-IDContentsSolvent system
140mM sodium phosphate, 50mM sodium chloride, 0.05% sodium azide, 0.3mM XACb0070, 90% H2O/10% D2O90% H2O/10% D2O
240mM sodium phosphate, 300mM sodium chloride, 0.05% sodium azide, 0.5mM XACb0070, 90% H2O/10% D2O90% H2O/10% D2O
340mM sodium phosphate, 300mM sodium chloride, 0.05% sodium azide, 0.5mM XACb0070, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentSolution-ID
40 mMsodium phosphate1
50 mMsodium chloride1
0.05 %sodium azide1
0.3 mMXACb00701
40 mMsodium phosphate2
300 mMsodium chloride2
0.05 %sodium azide2
0.5 mMXACb00702
40 mMsodium phosphate3
300 mMsodium chloride3
0.05 %sodium azide3
0.5 mMXACb00703
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
11706.7ambient atm313 K
24209ambient Pa308.0 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE4001
Bruker AvanceBrukerAVANCE7002

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMRBruker Biospincollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRView5Johnson, One Moon Scientificdata analysis
Xplor-NIHrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR constraintsNOE constraints total: 936 / NOE intraresidue total count: 58 / NOE long range total count: 28 / NOE medium range total count: 318 / NOE sequential total count: 380 / Hydrogen bond constraints total count: 106 / Protein chi angle constraints total count: 22 / Protein other angle constraints total count: 0 / Protein phi angle constraints total count: 90 / Protein psi angle constraints total count: 78
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 500 / Conformers submitted total number: 20 / Maximum lower distance constraint violation: 0.006 Å / Maximum torsion angle constraint violation: 0.505 ° / Maximum upper distance constraint violation: 0.03 Å / Representative conformer: 1
NMR ensemble rmsDistance rms dev: 0.0108 Å / Distance rms dev error: 0.0008 Å

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