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- PDB-1bbx: NON-SPECIFIC PROTEIN-DNA INTERACTIONS IN THE SSO7D-DNA COMPLEX, N... -

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Basic information

Entry
Database: PDB / ID: 1bbx
TitleNON-SPECIFIC PROTEIN-DNA INTERACTIONS IN THE SSO7D-DNA COMPLEX, NMR, 1 STRUCTURE
Components
  • DNA (5'-D(*CP*TP*AP*GP*CP*GP*CP*GP*CP*TP*AP*G)-3')
  • DNA-BINDING PROTEIN 7D
KeywordsDNA BINDING PROTEIN/DNA / PROTEIN-DNA INTERACTION / NONSPECIFIC PROTEIN-DNA INTERACTION / COMPLEX (DNA-BINDING PROTEIN-DNA) / DNA BINDING PROTEIN-DNA COMPLEX
Function / homology
Function and homology information


RNA endonuclease activity / DNA binding / cytoplasm
Similarity search - Function
DNA-binding 7kDa protein / 7kD DNA-binding domain / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #40 / Chromo-like domain superfamily / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / DNA-binding protein 7d
Similarity search - Component
Biological speciesSulfolobus solfataricus (archaea)
MethodSOLUTION NMR / simulated annealing
AuthorsAgback, P. / Baumann, H. / Knapp, S. / Ladenstein, R. / Hard, T.
Citation
Journal: Nat.Struct.Biol. / Year: 1998
Title: Architecture of Nonspecific Protein-DNA Interactions in the Sso7D-DNA Complex
Authors: Agback, P. / Baumann, H. / Knapp, S. / Ladenstein, R. / Hard, T.
#1: Journal: J.Mol.Biol. / Year: 1995
Title: DNA-Binding Surface of the Sso7D Protein from Sulfolobus Solfataricus
Authors: Baumann, H. / Knapp, S. / Karshikoff, A. / Ladenstein, R. / Hard, T.
#2: Journal: Nat.Struct.Biol. / Year: 1994
Title: Solution Structure and DNA-Binding Properties of a Thermostable Protein from the Archaeon Sulfolobus Solfataricus
Authors: Baumann, H. / Knapp, S. / Lundback, T. / Ladenstein, R. / Hard, T.
History
DepositionApr 24, 1998Processing site: BNL
Revision 1.0Oct 14, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 16, 2022Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list / 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.process_site / _struct_ref_seq_dif.details
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA (5'-D(*CP*TP*AP*GP*CP*GP*CP*GP*CP*TP*AP*G)-3')
B: DNA (5'-D(*CP*TP*AP*GP*CP*GP*CP*GP*CP*TP*AP*G)-3')
C: DNA-BINDING PROTEIN 7D
D: DNA-BINDING PROTEIN 7D


Theoretical massNumber of molelcules
Total (without water)21,6544
Polymers21,6544
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)1 / 50LOWEST RESTRAINT ENERGY
Representative

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Components

#1: DNA chain DNA (5'-D(*CP*TP*AP*GP*CP*GP*CP*GP*CP*TP*AP*G)-3')


Mass: 3663.392 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Protein DNA-BINDING PROTEIN 7D / SSO7D


Mass: 7163.403 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus solfataricus (archaea) / Cell line: BL21 / Plasmid: PET15B / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P39476

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111HNCO
121CBCA(CO)NNH
131HN(CA)CB
141(H)CCH-TOCSY
151HCC-TOCSY
16113C
17115N DOUBLE HALF-FILTERED 2D NOESY
1812D NOESY
19115N-EDITED 3D NOE-HSQC
110113C-EDITED 3D NOE-HSQC
NMR detailsText: THE STRUCTURE WAS DETERMINED USING TRIPLE-RESONANCE NMR SPECTROSCOPY ON 13C, 15N-LABELLED SSO7D AND NON-LABELLED DNA

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Sample preparation

DetailsContents: H2O:D2O 9:1
Sample conditionsIonic strength: 60 mM / pH: 5 / Pressure: 1 atm / Temperature: 323 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: Varian UNITY / Manufacturer: Varian / Model: UNITY / Field strength: 500 MHz

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
X-PLOR3.1phasing
NMR software
NameVersionDeveloperClassification
X-PLOR3.1BRUNGERrefinement
VNMRstructure solution
ANSIGstructure solution
XPLORstructure solution
RefinementMethod: simulated annealing / Software ordinal: 1
Details: REFINEMENT DETAILS CAN BE FOUND IN THE JRNL CITATION ABOVE.
NMR ensembleConformer selection criteria: LOWEST RESTRAINT ENERGY / Conformers calculated total number: 50 / Conformers submitted total number: 1

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