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- PDB-2vkc: Solution structure of the B3BP Smr domain -

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Basic information

Entry
Database: PDB / ID: 2vkc
TitleSolution structure of the B3BP Smr domain
ComponentsNEDD4-BINDING PROTEIN 2
KeywordsHYDROLASE / HUMAN BCL3 BINDING PROTEIN / ALTERNATIVE SPLICING / HOMOLOGOUS RECOMBINATION / MISMATCH REPAIR / SMALL MUTS RELATED / NUCLEOTIDE-BINDING / ATP-BINDING / UBL CONJUGATION / PHOSPHORYLATION / SMR / B3BP / CYTOPLASM / COILED COIL
Function / homology
Function and homology information


ATP-dependent polydeoxyribonucleotide 5'-hydroxyl-kinase activity / Hydrolases / ubiquitin binding / DNA endonuclease activity / endonuclease activity / ATP binding / cytosol
Similarity search - Function
Domain of unknown function DUF1771 / NEDD4-binding protein 2, CUE domain / Domain of unknown function (DUF1771) / DUF1771 / : / Ribosomal Protein S8; Chain: A, domain 1 - #110 / Smr domain / Small MutS-related domain / Smr domain superfamily / Smr domain ...Domain of unknown function DUF1771 / NEDD4-binding protein 2, CUE domain / Domain of unknown function (DUF1771) / DUF1771 / : / Ribosomal Protein S8; Chain: A, domain 1 - #110 / Smr domain / Small MutS-related domain / Smr domain superfamily / Smr domain / Smr domain profile. / Ubiquitin system component CUE / CUE domain profile. / AAA domain / Ribosomal Protein S8; Chain: A, domain 1 / UBA-like superfamily / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
NEDD4-binding protein 2
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodSOLUTION NMR / CANDID,PROXIES
AuthorsDiercks, T. / Ab, E. / Daniels, M.A. / deJong, R.N. / Besseling, R. / Kaptein, R. / Folkers, G.E.
CitationJournal: J.Mol.Biol. / Year: 2008
Title: Solution Structure and Characterization of the DNA- Binding Activity of the B3BP-Smr Domain.
Authors: Diercks, T. / Ab, E. / Daniels, M.A. / De Jong, R.N. / Besseling, R. / Kaptein, R. / Folkers, G.E.
History
DepositionDec 18, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 14, 2008Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0May 15, 2024Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Other
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_mr

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NEDD4-BINDING PROTEIN 2


Theoretical massNumber of molelcules
Total (without water)15,1901
Polymers15,1901
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)28 / 250QUALITY
RepresentativeModel #1

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Components

#1: Protein NEDD4-BINDING PROTEIN 2 / N4BP2 / BCL-3-BINDING PROTEIN / B3BP SMR DOMAIN


Mass: 15189.629 Da / Num. of mol.: 1 / Fragment: RESIDUES 1666-1770
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q86UW6

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111HCH-NOESY
121HNH-NOESY
131CNH- NOESY
1412D-NON-NOESY
1512D- NOESY
NMR detailsText: NONE

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Sample preparation

DetailsContents: 95% WATER/5% D2O
Sample conditionsIonic strength: 200 mM / pH: 6 / Pressure: 1.0 atm / Temperature: 308.0 K

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NMR measurement

NMR spectrometerType: Bruker DMX / Manufacturer: Bruker / Model: DMX / Field strength: 700 MHz

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Processing

NMR software
NameDeveloperClassification
CNSBRUNGER,ADAMS,CLORE,DELANO,GROS, GROSSE- KUNSTLEVE,JIANG,KUSZEWSKI,NILGES, PANNU,READ, RICE,SIMONSON,WARRENrefinement
CYANAstructure solution
RefinementMethod: CANDID,PROXIES / Software ordinal: 1 / Details: RECORD PROTOCOL
NMR ensembleConformer selection criteria: QUALITY / Conformers calculated total number: 250 / Conformers submitted total number: 28

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