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- PDB-2eqk: Solution structure of the TUDOR domain of Tudor domain-containing... -

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Basic information

Entry
Database: PDB / ID: 2eqk
TitleSolution structure of the TUDOR domain of Tudor domain-containing protein 4
ComponentsTudor domain-containing protein 4
KeywordsTRANSCRIPTION / TUDOR domain / Tudor domain-containing protein 4 / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


spermatid development / identical protein binding / nucleus / metal ion binding / cytoplasm
Similarity search - Function
: / : / : / : / : / RING finger protein 17 / Tudor domain / Tudor domain profile. / Tudor domain / Tudor domain ...: / : / : / : / : / RING finger protein 17 / Tudor domain / Tudor domain profile. / Tudor domain / Tudor domain / SH3 type barrels. - #140 / SNase-like, OB-fold superfamily / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Zinc finger RING-type profile. / Zinc finger, RING-type / SH3 type barrels. / Roll / Mainly Beta
Similarity search - Domain/homology
RING finger protein 17 / RING finger protein 17
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsDang, W. / Muto, Y. / Inoue, M. / Kigawa, T. / Shirouzu, M. / Terada, T. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Solution structure of the TUDOR domain of Tudor domain-containing protein 4
Authors: Dang, W. / Muto, Y. / Inoue, M. / Kigawa, T. / Shirouzu, M. / Terada, T. / Yokoyama, S.
History
DepositionMar 30, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 2, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 9, 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
Revision 1.3May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Remark 650HELIX DETERMINATION METHOD: AUTHOR DETERMINED

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Tudor domain-containing protein 4


Theoretical massNumber of molelcules
Total (without water)9,7081
Polymers9,7081
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)20 / 100structures with the least restraint violations, structures with the lowest energy, target function
RepresentativeModel #1lowest energy

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Components

#1: Protein Tudor domain-containing protein 4


Mass: 9708.189 Da / Num. of mol.: 1 / Fragment: TUDOR domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: Cell free protein synthesis / Gene: TDRD4 / Plasmid: P060911-18 / References: UniProt: Q9NUY9, UniProt: Q9BXT8*PLUS

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Experimental details

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Experiment

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

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Sample preparation

DetailsContents: 1.0mM 13C, 15N-labeled protein; 20mM d-Tris-HCl (pH 7.0); 100mM NaCl; 1mM d-DTT; 0.02% NaN3; 90% H2O, 10% D2O
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 120mM / pH: 7 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2.6Brukercollection
NMRPipe20031121Delaglio,F.processing
NMRView5.0.4Johnson,B.A.data analysis
KUJIRA0.9814Kobayashi,N.data analysis
CYANA2.0.17Guntert,P.structure solution
CYANA2.0.17Guntert,P.refinement
RefinementMethod: torsion angle 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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