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- PDB-1iuf: LOW RESOLUTION SOLUTION STRUCTURE OF THE TWO DNA-BINDING DOMAINS ... -

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Basic information

Entry
Database: PDB / ID: 1iuf
TitleLOW RESOLUTION SOLUTION STRUCTURE OF THE TWO DNA-BINDING DOMAINS IN Schizosaccharomyces pombe ABP1 PROTEIN
Componentscentromere abp1 protein
KeywordsDNA BINDING PROTEIN / centromere / RIKEN Structural Genomics/Proteomics Initiative / RSGI / Structural Genomics
Function / homology
Function and homology information


protein localization to mating-type region heterochromatin / donor selection / condensed chromosome, centromeric region => GO:0000779 / mating-type region heterochromatin / centromeric DNA binding / chromatin => GO:0000785 / mitotic sister chromatid segregation / sequence-specific DNA binding / DNA binding / nucleus
Similarity search - Function
ARS-binding protein 1, N-terminal / Fission yeast centromere protein N-terminal domain / DDE superfamily endonuclease domain / HTH CenpB-type DNA-binding domain / DDE superfamily endonuclease / Tc5 transposase DNA-binding domain / CENPB-type HTH domain profile. / Putative DNA-binding domain in centromere protein B, mouse jerky and transposases. / Homeodomain-like / Homeobox-like domain superfamily ...ARS-binding protein 1, N-terminal / Fission yeast centromere protein N-terminal domain / DDE superfamily endonuclease domain / HTH CenpB-type DNA-binding domain / DDE superfamily endonuclease / Tc5 transposase DNA-binding domain / CENPB-type HTH domain profile. / Putative DNA-binding domain in centromere protein B, mouse jerky and transposases. / Homeodomain-like / Homeobox-like domain superfamily / Arc Repressor Mutant, subunit A / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
ARS-binding protein 1
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
MethodSOLUTION NMR / torsion angle dynamics followed with simulated annealing
AuthorsKikuchi, J. / Iwahara, J. / Kigawa, T. / Murakami, Y. / Okazaki, T. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: J.Biomol.NMR / Year: 2002
Title: Solution structure determination of the two DNA-binding domains in the Schizosaccharomyces pombe Abp1 protein by a combination of dipolar coupling and diffusion anisotropy restraints.
Authors: Kikuchi, J. / Iwahara, J. / Kigawa, T. / Murakami, Y. / Okazaki, T. / Yokoyama, S.
History
DepositionMar 4, 2002Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 5, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Dec 27, 2023Group: 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: centromere abp1 protein


Theoretical massNumber of molelcules
Total (without water)17,0861
Polymers17,0861
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)1 / 10structures with the lowest energy
RepresentativeModel #1

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Components

#1: Protein centromere abp1 protein / ARS-binding protein 1


Mass: 17086.396 Da / Num. of mol.: 1 / Fragment: N-terminal domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast)
Plasmid: pGADe / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P49777

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experimentType: 4D 13C/15N-separated NOESY
NMR detailsText: The structure was determined using triple-resonance NMR spectroscopy.

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Sample preparation

DetailsContents: 1mM Abp1 U-15N, 13C; 50mM Tris buffer; 90% H2O, 10% D2O
Sample conditionsIonic strength: 50mM / pH: 6.8 / Pressure: 1 atm / Temperature: 310 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 600 MHz

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Processing

NMR softwareName: CNS / Version: 1 / Developer: Brunger, A.T. et al. / Classification: refinement
RefinementMethod: torsion angle dynamics followed with simulated annealing
Software ordinal: 1
Details: residual sipolar coupling data were measured in pf1 phage liquid crystal diffusion anisotropy restraints were measured in solution
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 10 / Conformers submitted total number: 1

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