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- PDB-2jsp: The prokaryotic Cys2His2 zinc finger adopts a novel fold as revea... -

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Basic information

Entry
Database: PDB / ID: 2jsp
TitleThe prokaryotic Cys2His2 zinc finger adopts a novel fold as revealed by the NMR structure of A. tumefaciens Ros DNA binding domain
ComponentsTranscriptional regulatory protein ros
KeywordsGENE REGULATION / prokaryotic Cys2His2 zinc finger
Function / homology
Function and homology information


regulation of DNA-templated transcription / DNA binding / zinc ion binding
Similarity search - Function
ROS/MUCR transcriptional regulator protein / ROS/MUCR transcriptional regulator / ROS/MUCR transcriptional regulator superfamily / ROS/MUCR transcriptional regulator protein / Arc Repressor Mutant, subunit A / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Transcriptional regulatory protein ros
Similarity search - Component
Biological speciesAgrobacterium tumefaciens (bacteria)
MethodSOLUTION NMR / simulated annealing
AuthorsMalgieri, G.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2007
Title: The prokaryotic Cys2His2 zinc-finger adopts a novel fold as revealed by the NMR structure of Agrobacterium tumefaciens Ros DNA-binding domain.
Authors: Malgieri, G. / Russo, L. / Esposito, S. / Baglivo, I. / Zaccaro, L. / Pedone, E.M. / Di Blasio, B. / Isernia, C. / Pedone, P.V. / Fattorusso, R.
History
DepositionJul 10, 2007Deposition site: BMRB / Processing site: RCSB
Revision 1.0Oct 16, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 19, 2020Group: Data collection / Derived calculations / Other
Category: pdbx_database_status / pdbx_nmr_software ...pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 1.3May 1, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Transcriptional regulatory protein ros


Theoretical massNumber of molelcules
Total (without water)9,9541
Polymers9,9541
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein Transcriptional regulatory protein ros


Mass: 9954.439 Da / Num. of mol.: 1 / Fragment: DNA binding domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Agrobacterium tumefaciens (bacteria) / Gene: ros / Plasmid: pET-11d / Production host: Escherichia coli (E. coli) / References: UniProt: Q04152

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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-15N HSQC
1322D 1H-13C HSQC
1432D 1H-1H NOESY
1523D CBCA(CO)NH
1623D CBCANH
1723D HNCO
1823D HNCA
1913D HNHA
11023D 1H-13C NOESY
11113D 1H-15N NOESY
11223D CCH-TOCSY
11313D 1H-15N TOCSY
11432D 1H-1H TOCSY
11522D 1H-15N HSQC IPAP
11622D 1H-15N HSQC IPAP

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Sample preparation

Details
Solution-IDContentsSolvent system
11 mM [U-100% 15N] Ros87, 90% H2O/10% D2O90% H2O/10% D2O
21 mM [U-100% 13C; U-100% 15N] Ros87, 90% H2O/10% D2O90% H2O/10% D2O
31 mM Ros87, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMRos87[U-100% 15N]1
1 mMRos87[U-100% 13C; U-100% 15N]2
1 mMRos873
Sample conditionsIonic strength: 0.2 / pH: 6.8 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA5001
Varian INOVAVarianINOVA6002
Bruker AvanceBrukerAVANCE5003
Bruker AvanceBrukerAVANCE8004

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Processing

NMR software
NameDeveloperClassification
VnmrJVariancollection
XEASYBartels, C. et al.data analysis
Procheck-NMRLaskowski, R.A. et al.data analysis
ModelFreePalmer III, A.G. et al.data analysis
MOLMOLKoradi, R. et al.data analysis
SPDBGuex, N. et al.data analysis
CYANAGuntert, P. et al.refinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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