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- PDB-1wjr: Solution structure of the 2nd mbt domain from human KIAA1617 protein -

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Basic information

Entry
Database: PDB / ID: 1wjr
TitleSolution structure of the 2nd mbt domain from human KIAA1617 protein
ComponentsKIAA1617 protein
KeywordsPROTEIN BINDING / mbt domain / KIAA1617 protein / structural genomics / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


aggresome / transcription corepressor activity / histone binding / nuclear body / nuclear speck / negative regulation of gene expression / intracellular membrane-bounded organelle / negative regulation of DNA-templated transcription / chromatin binding / nucleoplasm ...aggresome / transcription corepressor activity / histone binding / nuclear body / nuclear speck / negative regulation of gene expression / intracellular membrane-bounded organelle / negative regulation of DNA-templated transcription / chromatin binding / nucleoplasm / nucleus / cytosol
Similarity search - Function
Scm-like with four MBT domains protein 1/2, SAM domain / SLED domain / SLED domain superfamily / SLED domain / Mbt repeat / MBT repeat profile. / Present in Drosophila Scm, l(3)mbt, and vertebrate SCML2 / mbt repeat / SAM domain (Sterile alpha motif) / SH3 type barrels. - #140 ...Scm-like with four MBT domains protein 1/2, SAM domain / SLED domain / SLED domain superfamily / SLED domain / Mbt repeat / MBT repeat profile. / Present in Drosophila Scm, l(3)mbt, and vertebrate SCML2 / mbt repeat / SAM domain (Sterile alpha motif) / SH3 type barrels. - #140 / Sterile alpha motif. / Sterile alpha motif domain / Sterile alpha motif/pointed domain superfamily / SH3 type barrels. / Roll / Mainly Beta
Similarity search - Domain/homology
Scm-like with four MBT domains protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics, restrained molecular dynamics
AuthorsTomizawa, T. / Kigawa, T. / Koshiba, S. / Inoue, M. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Solution structure of the 2nd mbt domain from human KIAA1617 protein
Authors: Tomizawa, T. / Kigawa, T. / Koshiba, S. / Inoue, M. / Yokoyama, S.
History
DepositionMay 29, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 29, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 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 / struct_ref_seq_dif
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 / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: KIAA1617 protein


Theoretical massNumber of molelcules
Total (without water)14,4521
Polymers14,4521
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)20 / 100structures with the least restraint violations, structures with the lowest energy, target function
RepresentativeModel #1lowest energy

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Components

#1: Protein KIAA1617 protein


Mass: 14452.286 Da / Num. of mol.: 1 / Fragment: mbt domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: Cell-free protein synthesis / Gene: KAZUSA cDNA fj13890 / Plasmid: P040119-21 / References: UniProt: Q5VUG0

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 13C-separated NOESY
1213D 15N-separated NOESY

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Sample preparation

DetailsContents: 1.14mM mbt domain U-15N,13C; 20mM d-Tris-HCl(pH 7.0); 100mM NaCl; 1mM d-DTT; 0.02% NaN3; 10% D2O
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 120mM / pH: 7.0 / Pressure: ambient / Temperature: 298 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2.6Brukercollection
NMRPipe20030801Delaglio, F.processing
NMRView5.0.4Johnson, B.A.data analysis
KUJIRA0.901Kobayashi, N.data analysis
CYANA2.0.17Guentert, P.structure solution
CYANA2.0.17Guentert, P.refinement
RefinementMethod: torsion angle dynamics, restrained molecular dynamics
Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations, structures with the lowest energy, target function
Conformers calculated total number: 100 / Conformers submitted total number: 20

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