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- PDB-2jqt: Structure of the bacterial replication origin-associated protein Cnu -

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Basic information

Entry
Database: PDB / ID: 2jqt
TitleStructure of the bacterial replication origin-associated protein Cnu
ComponentsH-NS/stpA-binding protein 2
KeywordsPROTEIN BINDING / Cnu / YdgT / replication origin associated / oriC / H-NS
Function / homology
Function and homology information


positive regulation of termination of DNA-templated transcription / negative regulation of single-species biofilm formation on inanimate substrate / DNA binding
Similarity search - Function
HHA / Haemolysin expression modulating, HHA / HHA superfamily / Haemolysin expression modulating protein / Monooxygenase / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
OriC-binding nucleoid-associated protein
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsBae, S.H. / Liu, D. / Lim, H.M. / Lee, Y. / Choi, B.S.
CitationJournal: Biochemistry / Year: 2008
Title: Structure of the nucleoid-associated protein Cnu reveals common binding sites for H-NS in Cnu and Hha.
Authors: Bae, S.H. / Liu, D. / Lim, H.M. / Lee, Y. / Choi, B.S.
History
DepositionJun 7, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 22, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 9, 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 1.3Dec 20, 2023Group: Data collection / Other
Category: chem_comp_atom / chem_comp_bond / pdbx_database_status
Item: _pdbx_database_status.deposit_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: H-NS/stpA-binding protein 2


Theoretical massNumber of molelcules
Total (without water)8,4291
Polymers8,4291
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein H-NS/stpA-binding protein 2


Mass: 8428.572 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: ydgT / Production host: Escherichia coli (E. coli) / References: UniProt: P64467

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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 HN(CA)CB
1513D HNCO
1613D (H)CCH-COSY
1713D (H)CCH-TOCSY
1813D HBHA(CO)NH
1913D 1H-15N NOESY
11013D 1H-13C NOESY

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Sample preparation

DetailsContents: 0.4-0.8 mM [U-15N] cnu, 0.4-0.8 mM [U-13C; U-15N] cnu, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.4 mMcnu-1[U-15N]1
0.4 mMcnu-2[U-13C; U-15N]1
Sample conditionsIonic strength: 0.02 / pH: 7.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

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Processing

NMR software
NameDeveloperClassification
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
SparkyGoddardchemical shift assignment
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
CNSBrunger, Adams, Clore, Gros, Nilges and Readstructure solution
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 10

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