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- PDB-2lqr: NMR structure of Ig3 domain of palladin -

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Basic information

Entry
Database: PDB / ID: 2lqr
TitleNMR structure of Ig3 domain of palladin
ComponentsPalladin
KeywordsPROTEIN BINDING / actin binding protein / immunoglubulin
Function / homology
Function and homology information


axon guidance receptor activity / epithelial cell morphogenesis / ruffle organization / podosome / positive regulation of podosome assembly / keratinocyte development / homophilic cell adhesion via plasma membrane adhesion molecules / excitatory synapse / axonal growth cone / stress fiber ...axon guidance receptor activity / epithelial cell morphogenesis / ruffle organization / podosome / positive regulation of podosome assembly / keratinocyte development / homophilic cell adhesion via plasma membrane adhesion molecules / excitatory synapse / axonal growth cone / stress fiber / ruffle / cytoskeletal protein binding / filopodium / actin filament / synapse organization / Z disc / neuron projection development / actin cytoskeleton / cell migration / lamellipodium / actin binding / growth cone / actin cytoskeleton organization / cytoskeleton / axon / focal adhesion / neuronal cell body / nucleus / plasma membrane / cytosol
Similarity search - Function
Palladin, C-terminal immunoglobulin-like domain / Basigin-like / Immunoglobulin I-set / Immunoglobulin I-set domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain ...Palladin, C-terminal immunoglobulin-like domain / Basigin-like / Immunoglobulin I-set / Immunoglobulin I-set domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / 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
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / simulated annealing, torsion angle dynamics, matrix relaxation
Model detailsfewest violations, model 1
AuthorsBeck, M.R. / Dixon IV, R.D.S. / Otey, C.A. / Campbell, S.L. / Murphy, G.S.
CitationJournal: J.Mol.Biol. / Year: 2013
Title: Structure and Function of Palladin's Actin Binding Domain.
Authors: Beck, M.R. / Dixon, R.D. / Goicoechea, S.M. / Murphy, G.S. / Brungardt, J.G. / Beam, M.T. / Srinath, P. / Patel, J. / Mohiuddin, J. / Otey, C.A. / Campbell, S.L.
History
DepositionMar 13, 2012Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jan 23, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 26, 2013Group: Database references
Revision 1.2Jul 24, 2013Group: Database references
Revision 1.3Sep 11, 2013Group: Database references
Revision 1.4May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / 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: Palladin


Theoretical massNumber of molelcules
Total (without water)11,9921
Polymers11,9921
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 / 20structures with the lowest energy
RepresentativeModel #1fewest violations

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Components

#1: Antibody Palladin


Mass: 11991.606 Da / Num. of mol.: 1 / Fragment: Ig-like C2-type 3 domain residues 1022-1126
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Palld, Kiaa0992 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 RIPL / References: UniProt: Q9ET54

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D 1H-15N NOESY
1313D 1H-13C NOESY aliphatic
1413D 1H-13C NOESY aromatic

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Sample preparation

DetailsContents: 50 mM TRIS-maleate, 150 mM NaCl, 2 mM DTT, 0.01 % sodium azide, 10 % D2O, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentSolution-ID
50 mMTRIS-maleate-11
150 mMNaCl-21
2 mMDTT-31
0.01 %sodium azide-41
10 %D2O-51
Sample conditionsIonic strength: 150 / pH: 6.0 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA7001
Varian INOVAVarianINOVA6002

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Processing

NMR software
NameVersionDeveloperClassification
NMRViewJohnson, One Moon Scientificpeak picking
NMRViewJohnson, One Moon Scientificprocessing
NMRViewJohnson, One Moon Scientificchemical shift assignment
NMRDrawDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
CYANA2.2Guntert, Mumenthaler and Wuthrichstructure solution
PSVSBhattacharya and Montelionedata analysis
RosettaRASRECO.F. Lange and D. Bakerrefinement
CYANAGuntert, Mumenthaler and Wuthrichrefinement
RefinementMethod: simulated annealing, torsion angle dynamics, matrix relaxation
Software ordinal: 1
Details: RASREC method has six stages that cycle between generating Rosetta fragments, producing low energy models, and biasing conformational search space towards low energy space
NMR constraintsNOE constraints total: 1395 / NOE intraresidue total count: 167 / NOE long range total count: 748 / NOE medium range total count: 150 / NOE sequential total count: 330
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 20 / Conformers submitted total number: 20

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