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- PDB-2ev8: Solution structure of the erythroid p55 PDZ domain -

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Basic information

Entry
Database: PDB / ID: 2ev8
TitleSolution structure of the erythroid p55 PDZ domain
Components55 kDa erythrocyte membrane protein
KeywordsMEMBRANE PROTEIN / MAGUK / p55 / PDZ
Function / homology
Function and homology information


regulation of neutrophil chemotaxis / guanylate kinase activity / stereocilium / Sensory processing of sound by outer hair cells of the cochlea / cortical cytoskeleton / centriolar satellite / cell-cell junction / signaling receptor binding / signal transduction / membrane / plasma membrane
Similarity search - Function
MPP1, SH3 domain / Guanylate kinase, conserved site / Guanylate kinase-like signature. / Guanylate kinase-like domain profile. / Guanylate kinase-like domain / Guanylate kinase/L-type calcium channel beta subunit / Guanylate kinase / Guanylate kinase homologues. / PDZ domain / Pdz3 Domain ...MPP1, SH3 domain / Guanylate kinase, conserved site / Guanylate kinase-like signature. / Guanylate kinase-like domain profile. / Guanylate kinase-like domain / Guanylate kinase/L-type calcium channel beta subunit / Guanylate kinase / Guanylate kinase homologues. / PDZ domain / Pdz3 Domain / PDZ domain / SH3 domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Roll / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta
Similarity search - Domain/homology
55 kDa erythrocyte membrane protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsKusunoki, H. / Kohno, T.
CitationJournal: Proteins / Year: 2006
Title: Solution structure of human erythroid p55 PDZ domain
Authors: Kusunoki, H. / Kohno, T.
History
DepositionOct 31, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 10, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 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_spectrometer ...database_2 / 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_spectrometer.model / _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: 55 kDa erythrocyte membrane protein


Theoretical massNumber of molelcules
Total (without water)10,9491
Polymers10,9491
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
RepresentativeModel #1lowest energy

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Components

#1: Protein 55 kDa erythrocyte membrane protein / erythroid p55 / p55 / Membrane protein / palmitoylated 1


Mass: 10948.651 Da / Num. of mol.: 1 / Fragment: PDZ domain, Residues 69-153
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3) / References: UniProt: Q00013

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1223D 15N-separated NOESY
132HNHB
1433D 13C-separated NOESY
153HN(CO)HB
163HN(CO)C

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Sample preparation

Details
Solution-IDContentsSolvent system
11.2mM p55 PDZ, 20mM Sodium phosphate, 41mM NaCl, 0.8mM DTT, 9% glycerol-d590% H2O/10% D2O
21.1mM p55 PDZ U-15N, 20mM Sodium phosphate, 41mM NaCl, 0.8mM DTT, 9% glycerol-d590% H2O/10% D2O
31.5mM p55 PDZ U-13C, 15N, 20mM Sodium phosphate, 41mM NaCl, 0.8mM DTT, 9% glycerol-d590% H2O/10% D2O
Sample conditionspH: 6.8 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 500 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CNS1.1Brungerstructure solution
CNS1.1Brungerrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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