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- PDB-2edu: Solution structure of RSGI RUH-070, a C-terminal domain of kinesi... -

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Basic information

Entry
Database: PDB / ID: 2edu
TitleSolution structure of RSGI RUH-070, a C-terminal domain of kinesin-like protein KIF22 from human cDNA
ComponentsKinesin-like protein KIF22
KeywordsTRANSPORT PROTEIN / kinesin / kinesin-like 4 / kinesin-like DNA binding domain / helix turn helix motif / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


metaphase chromosome alignment / Kinesins / sister chromatid cohesion / COPI-dependent Golgi-to-ER retrograde traffic / kinesin complex / microtubule motor activity / mitotic metaphase chromosome alignment / microtubule-based movement / MHC class II antigen presentation / mitotic spindle ...metaphase chromosome alignment / Kinesins / sister chromatid cohesion / COPI-dependent Golgi-to-ER retrograde traffic / kinesin complex / microtubule motor activity / mitotic metaphase chromosome alignment / microtubule-based movement / MHC class II antigen presentation / mitotic spindle / kinetochore / mitotic cell cycle / microtubule binding / microtubule / nuclear speck / DNA repair / chromatin / ATP hydrolysis activity / DNA binding / ATP binding / nucleus / cytosol
Similarity search - Function
AF1531-like domain / Helix-hairpin-helix motif / Kinesin-like protein / RuvA domain 2-like / Kinesin motor domain signature. / Kinesin motor domain, conserved site / Kinesin motor domain / Kinesin motor domain profile. / Kinesin motor, catalytic domain. ATPase. / Kinesin motor domain ...AF1531-like domain / Helix-hairpin-helix motif / Kinesin-like protein / RuvA domain 2-like / Kinesin motor domain signature. / Kinesin motor domain, conserved site / Kinesin motor domain / Kinesin motor domain profile. / Kinesin motor, catalytic domain. ATPase. / Kinesin motor domain / Helix-hairpin-helix DNA-binding motif, class 1 / Helix-hairpin-helix DNA-binding motif class 1 / Kinesin motor domain superfamily / DNA polymerase; domain 1 / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Kinesin-like protein KIF22
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsAbe, T. / Hirota, H. / Hayashi, F. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Solution structure of RSGI RUH-070, a C-terminal domain of kinesin-like protein KIF22 from human cDNA
Authors: Abe, T. / Hirota, H. / Hayashi, F. / Yokoyama, S.
History
DepositionFeb 15, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 21, 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_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 / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Kinesin-like protein KIF22


Theoretical massNumber of molelcules
Total (without water)10,7091
Polymers10,7091
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 and target function

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Components

#1: Protein Kinesin-like protein KIF22 / Kinesin-like DNA-binding protein / Kinesin-like protein 4


Mass: 10709.113 Da / Num. of mol.: 1 / Fragment: C-terminal domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: Cell-free protein synthesis / Gene: KIF22 / Plasmid: P060327-23 / References: UniProt: Q14807

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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
NMR detailsText: Spectrometer_id 1 for 3D_13C-separated_NOESY; Spectrometer_id 2 for 3D_15N-separated_NOESY

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Sample preparation

DetailsContents: 1.16mM RSGI RUH-070 U-15N, 13C; 20mM d-Tris-HCl; 1mM d-DTT; 0.02% NaN3; 90% H2O, 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

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA9001
Varian INOVAVarianINOVA8002

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Processing

NMR software
NameVersionDeveloperClassification
VNMR6.1CVariancollection
NMRPipe20060524Delaglio, F.processing
NMRView5.0.4Johnson, B. A.data analysis
KUJIRA0.982Kobayashi, N.data analysis
CYANA2.0.17Guntert, P.refinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy and target function
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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