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- PDB-2dlp: Solution structure of the SH3 domain of human KIAA1783 protein -

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Basic information

Entry
Database: PDB / ID: 2dlp
TitleSolution structure of the SH3 domain of human KIAA1783 protein
ComponentsKIAA1783 protein
KeywordsSTRUCTURAL PROTEIN / SH3 domain / KIAA1783 protein / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


plasma membrane bounded cell projection / myosin complex / cytoskeletal motor activity / actin binding / ATP binding / cytoplasm
Similarity search - Function
MYO15B, SH3 domain / Myosin-XV, FERM domain C-lobe / : / MyTH4 domain / MyTH4 domain superfamily / MyTH4 domain / MyTH4 domain profile. / Domain in Myosin and Kinesin Tails / Variant SH3 domain / FERM central domain ...MYO15B, SH3 domain / Myosin-XV, FERM domain C-lobe / : / MyTH4 domain / MyTH4 domain superfamily / MyTH4 domain / MyTH4 domain profile. / Domain in Myosin and Kinesin Tails / Variant SH3 domain / FERM central domain / FERM/acyl-CoA-binding protein superfamily / Myosin head, motor domain / Myosin head (motor domain) / Myosin motor domain profile. / Myosin. Large ATPases. / IQ motif profile. / SH3 Domains / FERM central domain / FERM superfamily, second domain / FERM domain / FERM domain profile. / Band 4.1 domain / Band 4.1 homologues / Kinesin motor domain superfamily / ATP synthase alpha and beta subunits signature. / SH3 type barrels. / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / PH-like domain superfamily / Roll / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta
Similarity search - Domain/homology
Unconventional myosin-XVB
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsQin, X.R. / Kurosaki, C. / Yoshida, M. / Hayashi, F. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be published
Title: Solution structure of the SH3 domain of human KIAA1783 protein
Authors: Qin, X.R. / Kurosaki, C. / Yoshida, M. / Hayashi, F. / Yokoyama, S.
History
DepositionApr 20, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 20, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 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
Revision 1.4May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: KIAA1783 protein


Theoretical massNumber of molelcules
Total (without water)8,6851
Polymers8,6851
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 / 100target function, structures with the lowest energy, structures with the least restraint violations
RepresentativeModel #1lowest energy

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Components

#1: Protein KIAA1783 protein


Mass: 8684.576 Da / Num. of mol.: 1 / Fragment: SH3 domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: cell free protein synthesis / Gene: KIAA1783 / Plasmid: P051101-05 / Production host: Cell free synthesis / References: UniProt: Q96JP2

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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: 1.15mM 13C, 15N-labeled protein; 20mM d-Tris-HCl(pH7.0); 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: JEOL ECA / Manufacturer: JEOL / Model: ECA / Field strength: 700 MHz

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Processing

NMR software
NameVersionDeveloperClassification
Delta4.3JEOLcollection
NMRPipe20031121Delaglio, F.processing
NMRView5.0.4Johnson, B.Adata analysis
KUJIRA0.9296Kobayashi, 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: target function, structures with the lowest energy, structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 20

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