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- PDB-1yua: C-TERMINAL DOMAIN OF ESCHERICHIA COLI TOPOISOMERASE I -

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Basic information

Entry
Database: PDB / ID: 1yua
TitleC-TERMINAL DOMAIN OF ESCHERICHIA COLI TOPOISOMERASE I
ComponentsTOPOISOMERASE ITOP1
KeywordsDNA BINDING PROTEIN / GENE-REGULATING PROTEIN
Function / homology
Function and homology information


DNA topoisomerase activity / DNA topoisomerase / DNA topoisomerase type I (single strand cut, ATP-independent) activity / DNA topological change / chromosome / DNA binding / metal ion binding / cytosol
Similarity search - Function
Bacterial Topoisomerase I; domain 1 / Bacterial Topoisomerase I, domain 1 / DNA topoisomerase I, zinc ribbon-like, bacterial-type / : / Topoisomerase I zinc-ribbon-like / Topoisomerase I, zinc finger / DNA topoisomerase, type IA, zn finger / Topoisomerase DNA binding C4 zinc finger / DNA topoisomerase I, bacterial-type / DNA topoisomerase I, type IA ...Bacterial Topoisomerase I; domain 1 / Bacterial Topoisomerase I, domain 1 / DNA topoisomerase I, zinc ribbon-like, bacterial-type / : / Topoisomerase I zinc-ribbon-like / Topoisomerase I, zinc finger / DNA topoisomerase, type IA, zn finger / Topoisomerase DNA binding C4 zinc finger / DNA topoisomerase I, bacterial-type / DNA topoisomerase I, type IA / DNA topoisomerase 1, TOPRIM domain / DNA topoisomerase, type IA / DNA topoisomerase, type IA, central region, subdomain 2 / DNA topoisomerase, type IA, active site / Topoisomerase (Topo) IA-type active site signature. / Topoisomerase (Topo) IA-type catalytic domain profile. / DNA topoisomerase, type IA, domain 2 / DNA topoisomerase, type IA, DNA-binding domain / DNA topoisomerase, type IA, central / DNA topoisomerase, type IA, central region, subdomain 1 / DNA topoisomerase, type IA, central region, subdomain 3 / DNA topoisomerase, type IA, core domain / DNA topoisomerase / Bacterial DNA topoisomeraes I ATP-binding domain / Bacterial DNA topoisomerase I DNA-binding domain / TOPRIM / N-terminal domain of TfIIb - #10 / Toprim domain / Toprim domain profile. / N-terminal domain of TfIIb / TOPRIM domain / Single Sheet / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Biological speciesEscherichia coli (E. coli)
MethodSOLUTION NMR
AuthorsYu, L. / Zhu, C.-X. / Tse-Dinh, Y.-C. / Fesik, S.W.
CitationJournal: Biochemistry / Year: 1995
Title: Solution structure of the C-terminal single-stranded DNA-binding domain of Escherichia coli topoisomerase I.
Authors: Yu, L. / Zhu, C.X. / Tse-Dinh, Y.C. / Fesik, S.W.
History
DepositionMar 2, 1995Processing site: BNL
Revision 1.0Mar 8, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / pdbx_struct_assembly ...pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.4May 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

Downloads & links

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Assembly

Deposited unit
A: TOPOISOMERASE I


Theoretical massNumber of molelcules
Total (without water)13,8611
Polymers13,8611
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Atom site foot note1: CIS PROLINE - PRO 44 MODEL 1 / 2: CIS PROLINE - PRO 44 MODEL 2 / 3: CIS PROLINE - PRO 44 MODEL 3 / 4: CIS PROLINE - PRO 44 MODEL 4 / 5: CIS PROLINE - PRO 44 MODEL 5 / 6: CIS PROLINE - PRO 44 MODEL 6 / 7: CIS PROLINE - PRO 44 MODEL 7 / 8: CIS PROLINE - PRO 44 MODEL 8 / 9: CIS PROLINE - PRO 44 MODEL 9 / 10: CIS PROLINE - PRO 44 MODEL 10 / 11: CIS PROLINE - PRO 44 MODEL 11 / 12: CIS PROLINE - PRO 44 MODEL 12 / 13: CIS PROLINE - PRO 44 MODEL 13 / 14: CIS PROLINE - PRO 44 MODEL 14 / 15: CIS PROLINE - PRO 44 MODEL 15 / 16: CIS PROLINE - PRO 44 MODEL 16 / 17: CIS PROLINE - PRO 44 MODEL 17 / 18: CIS PROLINE - PRO 44 MODEL 18 / 19: CIS PROLINE - PRO 44 MODEL 19 / 20: CIS PROLINE - PRO 44 MODEL 20 / 21: CIS PROLINE - PRO 44 MODEL 21 / 22: CIS PROLINE - PRO 44 MODEL 22 / 23: CIS PROLINE - PRO 44 MODEL 23 / 24: CIS PROLINE - PRO 44 MODEL 24 / 25: CIS PROLINE - PRO 44 MODEL 25 / 26: CIS PROLINE - PRO 44 MODEL 26
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)26 / -
Representative

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Components

#1: Protein TOPOISOMERASE I / TOP1


Mass: 13860.677 Da / Num. of mol.: 1 / Fragment: 122 C-TERMINAL RESIDUES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: DH5AI / Plasmid: PJW312
Gene (production host): C-TERMINAL FRAGMENT OF ESCHERICHIA COLI TOPOISOMERASE I
Production host: Escherichia coli (E. coli) / References: UniProt: P06612, DNA topoisomerase

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR

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Sample preparation

Crystal grow
*PLUS
Method: other

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
NMR softwareName: X-PLOR / Developer: BRUNGER / Classification: refinement
NMR ensembleConformers submitted total number: 26

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