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- PDB-1ujt: Solution structure of the second fibronectin Type III domain of h... -

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Basic information

Entry
Database: PDB / ID: 1ujt
TitleSolution structure of the second fibronectin Type III domain of human KIAA1568 protein
ComponentsKIAA1568 protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / fibronectin type III domain / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


olfactory bulb interneuron development / apoptotic process involved in luteolysis / negative regulation of negative chemotaxis / Regulation of cortical dendrite branching / negative regulation of synapse assembly / heart induction / ROBO receptors bind AKAP5 / axon guidance receptor activity / Regulation of commissural axon pathfinding by SLIT and ROBO / endocardial cushion formation ...olfactory bulb interneuron development / apoptotic process involved in luteolysis / negative regulation of negative chemotaxis / Regulation of cortical dendrite branching / negative regulation of synapse assembly / heart induction / ROBO receptors bind AKAP5 / axon guidance receptor activity / Regulation of commissural axon pathfinding by SLIT and ROBO / endocardial cushion formation / Signaling by ROBO receptors / pulmonary valve morphogenesis / outflow tract septum morphogenesis / metanephros development / aortic valve morphogenesis / retinal ganglion cell axon guidance / axon midline choice point recognition / aorta development / ureteric bud development / positive regulation of axonogenesis / ventricular septum morphogenesis / positive regulation of Notch signaling pathway / homophilic cell adhesion via plasma membrane adhesion molecules / axolemma / cellular response to hormone stimulus / central nervous system development / axon guidance / brain development / cell-cell adhesion / Regulation of expression of SLITs and ROBOs / chemotaxis / cell surface / extracellular exosome / identical protein binding / plasma membrane
Similarity search - Function
Immunoglobulin domain / Immunoglobulin I-set / Immunoglobulin I-set domain / Fibronectin type III domain / Fibronectin type 3 domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin V-Type / Fibronectin type-III domain profile. / Fibronectin type III ...Immunoglobulin domain / Immunoglobulin I-set / Immunoglobulin I-set domain / Fibronectin type III domain / Fibronectin type 3 domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin V-Type / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Roundabout homolog 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsTochio, N. / Koshiba, S. / Kigawa, T. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Solution structure of the second fibronectin Type III domain of human KIAA1568 protein
Authors: Tochio, N. / Koshiba, S. / Kigawa, T. / Yokoyama, S.
History
DepositionAug 11, 2003Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 11, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 27, 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
Revision 1.4Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: KIAA1568 protein


Theoretical massNumber of molelcules
Total (without water)13,3501
Polymers13,3501
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 lowest energy, target function
RepresentativeModel #1lowest energy

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Components

#1: Protein KIAA1568 protein


Mass: 13349.906 Da / Num. of mol.: 1 / Fragment: FN3 domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: Cell-free protein synthesis / Gene: Kazusa cDNA fh22308 / Plasmid: P021007-59 / References: UniProt: Q9HCK4

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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
1312D TROSY HNCO

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Sample preparation

DetailsContents: 1.0mM FN3 domain U-15N,13C; 20mM phosphate buffer NA; 100mM NaCl; 0.02% NaN3; 10% D2O
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 120mM / pH: 6.0 / Pressure: ambient / Temperature: 298 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE8001
Bruker AVANCEBrukerAVANCE6002

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2.6Brukercollection
XwinNMR3.1Brukercollection
NMRPipe200204025Delaglio, F.processing
NMRView5.0.4Johnson, B.A.data analysis
KUJIRA0.816Kobayashi, N.data analysis
CYANA2.0.17Guentert, P.structure solution
CYANA2.0.17Guentert, P.refinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy, target function
Conformers calculated total number: 100 / Conformers submitted total number: 20

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