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- PDB-1dbd: E2 DNA-BINDING DOMAIN FROM PAPILLOMAVIRUS BPV-1 -

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Basic information

Entry
Database: PDB / ID: 1dbd
TitleE2 DNA-BINDING DOMAIN FROM PAPILLOMAVIRUS BPV-1
ComponentsREGULATORY PROTEIN E2
KeywordsGENE REGULATION / DNA-BINDING DOMAIN
Function / homology
Function and homology information


viral DNA genome replication / regulation of DNA replication / DNA replication / DNA-binding transcription factor activity / nucleotide binding / DNA-templated transcription / host cell nucleus / DNA binding
Similarity search - Function
Papillomavirus E2, C-terminal / Papillomavirus E2, N-terminal / Regulatory protein E2 / E2 regulatory, transactivation domain / E2 regulatory, transactivation domain, subdomain 1 / E2 regulatory, transactivation domain, subdomain 2 / E2 (early) protein, N terminal / E2 (early) protein, C terminal / E2/EBNA1, C-terminal / RRM (RNA recognition motif) domain ...Papillomavirus E2, C-terminal / Papillomavirus E2, N-terminal / Regulatory protein E2 / E2 regulatory, transactivation domain / E2 regulatory, transactivation domain, subdomain 1 / E2 regulatory, transactivation domain, subdomain 2 / E2 (early) protein, N terminal / E2 (early) protein, C terminal / E2/EBNA1, C-terminal / RRM (RNA recognition motif) domain / Nucleotide-binding alpha-beta plait domain superfamily / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Regulatory protein E2
Similarity search - Component
Biological speciesBovine papillomavirus type 1
MethodSOLUTION NMR / DG, SA
AuthorsVeeraraghavan, S. / Mello, C.C. / Androphy, E.J. / Baleja, J.D.
CitationJournal: Biochemistry / Year: 1999
Title: Structural correlates for enhanced stability in the E2 DNA-binding domain from bovine papillomavirus.
Authors: Veeraraghavan, S. / Mello, C.C. / Androphy, E.J. / Baleja, J.D.
History
DepositionMay 21, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0Jan 1, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
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: REGULATORY PROTEIN E2
B: REGULATORY PROTEIN E2


Theoretical massNumber of molelcules
Total (without water)22,4992
Polymers22,4992
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 / 20MINIMIZED AVERAGE
Representative

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Components

#1: Protein REGULATORY PROTEIN E2


Mass: 11249.722 Da / Num. of mol.: 2 / Fragment: DNA-BINDING DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bovine papillomavirus type 1 / Genus: Deltapapillomavirus / Species: Bovine papillomavirus - 1 / Strain: 1 / Plasmid: PET32 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) PLYSS / References: UniProt: P03122

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR

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Sample preparation

Sample conditionsIonic strength: 0.1 / pH: 5.75 / Pressure: 1 atm / Temperature: 308.3 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AMXBrukerAMX5001
Bruker AVANCEBrukerAVANCE6002

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Processing

NMR software
NameDeveloperClassification
X-PLORBRUNGERrefinement
Insightstructure solution
X-PLORstructure solution
RefinementMethod: DG, SA / Software ordinal: 1
NMR ensembleConformer selection criteria: MINIMIZED AVERAGE / Conformers calculated total number: 20 / Conformers submitted total number: 1

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