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- PDB-2v1n: SOLUTION STRUCTURE OF THE REGION 51-160 OF HUMAN KIN17 REVEALS A ... -

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Entry
Database: PDB / ID: 2v1n
TitleSOLUTION STRUCTURE OF THE REGION 51-160 OF HUMAN KIN17 REVEALS A WINGED HELIX FOLD
ComponentsPROTEIN KIN HOMOLOG
KeywordsNUCLEAR PROTEIN / KIN17 / WINGED HELIX MOTIF
Function / homology
Function and homology information


Protein methylation / mRNA processing / nuclear matrix / double-stranded DNA binding / DNA recombination / DNA replication / intracellular membrane-bounded organelle / DNA repair / DNA damage response / protein-containing complex ...Protein methylation / mRNA processing / nuclear matrix / double-stranded DNA binding / DNA recombination / DNA replication / intracellular membrane-bounded organelle / DNA repair / DNA damage response / protein-containing complex / DNA binding / RNA binding / nucleoplasm / nucleus / metal ion binding / cytoplasm
Similarity search - Function
DNA/RNA-binding protein Kin17, conserved domain / DNA/RNA-binding protein Kin17, WH-like domain / KIN17-like protein / DNA/RNA-binding protein KIN17, WH-like domain superfamily / KN17, SH3-like C-terminal domain / Kin17, KOW domain / Domain of Kin17 curved DNA-binding protein / KN17 SH3-like C-terminal domain / Domain of Kin17 curved DNA-binding protein / Zinc finger C2H2 superfamily ...DNA/RNA-binding protein Kin17, conserved domain / DNA/RNA-binding protein Kin17, WH-like domain / KIN17-like protein / DNA/RNA-binding protein KIN17, WH-like domain superfamily / KN17, SH3-like C-terminal domain / Kin17, KOW domain / Domain of Kin17 curved DNA-binding protein / KN17 SH3-like C-terminal domain / Domain of Kin17 curved DNA-binding protein / Zinc finger C2H2 superfamily / Zinc finger C2H2 type domain signature. / Arc Repressor Mutant, subunit A / Ribosomal protein L2, domain 2 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DNA/RNA-binding protein KIN17
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodSOLUTION NMR / SIMULATED ANNEALING USING CNS
AuthorsCarlier, L. / Le Maire, A. / Gondry, M. / Guilhaudis, L. / Milazzo, I. / Davoust, D. / Couprie, J. / Gilquin, B. / Zinn-Justin, S.
CitationJournal: Protein Sci. / Year: 2007
Title: Solution Structure of the Region 51-160 of Human Kin17 Reveals an Atypical Winged Helix Domain
Authors: Carlier, L. / Le Maire, A. / Gondry, M. / Guilhaudis, L. / Milazzo, I. / Davoust, D. / Couprie, J. / Gilquin, B. / Zinn-Justin, S.
History
DepositionMay 27, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 27, 2007Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 15, 2020Group: Data collection / Other / Category: pdbx_database_status / pdbx_nmr_software
Item: _pdbx_database_status.status_code_cs / _pdbx_database_status.status_code_mr / _pdbx_nmr_software.name
Revision 1.4May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.
Remark 700 SHEET DETERMINATION METHOD: AUTHOR PROVIDED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROTEIN KIN HOMOLOG


Theoretical massNumber of molelcules
Total (without water)13,6861
Polymers13,6861
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)12 / 400STRUCTURES WITH ACCEPTABLE COVALENT GEOMETRY, WITH THE LEAST RESTRAINT VIOLATIONS, WITH THE LOWEST ENERGY
RepresentativeModel #1

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Components

#1: Protein PROTEIN KIN HOMOLOG / KIN17


Mass: 13686.452 Da / Num. of mol.: 1 / Fragment: RESIDUES 51-160
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PEXP-TH5 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)ROSETTA PLYSS / References: UniProt: O60870
Sequence detailsBECAUSE OF THE CLONING STRATEGY, THE PEPTIDE RESULTING FROM THE CLEAVAGE COMPRISES AN ADDITIONAL N- ...BECAUSE OF THE CLONING STRATEGY, THE PEPTIDE RESULTING FROM THE CLEAVAGE COMPRISES AN ADDITIONAL N-TERMINAL GLYCINE

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
11115N-NOESY-HSQC
12113C-NOESY- HSQC ALIPHATIC
23113C-NOESY- HSQC AROMATIC
NMR detailsText: THE STRUCTURE WAS DETERMINATED USING TRIPLE- RESONANCE NMR SPECTROSCOPY ON 15N- AND 15N-13C- LABELED PROTEINS

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Sample preparation

DetailsContents: 90%WATER / 10%D2O
Sample conditions
Conditions-IDIonic strengthpHTemperature (K)
150MM PHOSPHATE , 150MM NACL 6.0 303.0 K
250MM PHOSPHATE , 150MM NACL 6.0 303.0 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA8001
Bruker DMXBrukerDMX6002

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Processing

NMR software
NameVersionDeveloperClassification
CNS1BRUNGER,ADAMS,CLORE,DELANO,GROS, GROSSE- KUNSTLEVE,JIANG,KUSZEWSKI,NILGES, PANNU,READ, RICE,SIMONSON,WARRENrefinement
NMRViewstructure solution
NMRPipestructure solution
Felixstructure solution
CNSstructure solution
RefinementMethod: SIMULATED ANNEALING USING CNS / Software ordinal: 1
Details: REFINEMENT DETAILS CAN BE FOUND IN THE JRNL CITATION ABOVE. THE REGIONS 3-15 AND 108-111 ARE DISORDERED
NMR ensembleConformer selection criteria: STRUCTURES WITH ACCEPTABLE COVALENT GEOMETRY, WITH THE LEAST RESTRAINT VIOLATIONS, WITH THE LOWEST ENERGY
Conformers calculated total number: 400 / Conformers submitted total number: 12

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