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- PDB-1wf7: Solution structure of the PDZ domain of Enigma homologue protein -

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Basic information

Entry
Database: PDB / ID: 1wf7
TitleSolution structure of the PDZ domain of Enigma homologue protein
ComponentsEnigma homologue protein
KeywordsStructural genomics / unknown function / PDZ domain / Enigma homologue protein / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


muscle structure development / cell growth involved in cardiac muscle cell development / muscle alpha-actinin binding / regulation of dendritic spine morphogenesis / actinin binding / regulation of synapse assembly / filamentous actin / stress fiber / cell projection / adherens junction ...muscle structure development / cell growth involved in cardiac muscle cell development / muscle alpha-actinin binding / regulation of dendritic spine morphogenesis / actinin binding / regulation of synapse assembly / filamentous actin / stress fiber / cell projection / adherens junction / protein kinase C binding / Z disc / presynapse / heart development / actin binding / actin cytoskeleton organization / postsynaptic density / membrane / metal ion binding / cytosol
Similarity search - Function
: / LIM zinc-binding domain signature. / LIM domain / Zinc-binding domain present in Lin-11, Isl-1, Mec-3. / Zinc finger, LIM-type / LIM domain profile. / PDZ domain / Pdz3 Domain / PDZ domain / PDZ domain profile. ...: / LIM zinc-binding domain signature. / LIM domain / Zinc-binding domain present in Lin-11, Isl-1, Mec-3. / Zinc finger, LIM-type / LIM domain profile. / PDZ domain / Pdz3 Domain / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Roll / Mainly Beta
Similarity search - Domain/homology
PDZ and LIM domain protein 5
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / torsion angle dynamic
AuthorsQin, X. / Tochio, N. / Kigawa, T. / Hayashi, F. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be published
Title: Solution structure of the PDZ domain of Enigma homologue protein
Authors: Qin, X. / Tochio, N. / Kigawa, T. / Hayashi, F. / Yokoyama, S.
History
DepositionMay 26, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 26, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 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_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: Enigma homologue protein


Theoretical massNumber of molelcules
Total (without water)10,3101
Polymers10,3101
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 / 100structures with the least restraint violations, structures with the lowest energy, target function
RepresentativeModel #1lowest energy

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Components

#1: Protein Enigma homologue protein


Mass: 10309.564 Da / Num. of mol.: 1 / Fragment: PDZ domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Description: cell free protein synthesis / Gene: RIKEN 1110001A05 / Plasmid: P030203-44 / References: UniProt: Q8CI51

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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

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Sample preparation

DetailsContents: 1.06mM 13C, 15N-labeled protein; 20mM PiNa(pH6.0); 100mM NaCl; 1mM d-DTT; 0.02% NaN3
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 120mM / pH: 6 / Pressure: ambient / Temperature: 298 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 800 MHz

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Processing

NMR software
NameVersionDeveloperClassification
VNMR6.1CVariancollection
NMRPipe20020425Delaglio.F.processing
NMRView5.0.4Johnson, B.A.data analysis
KUJIRA0.854Kobayashi, N.data analysis
CYANA1.0.7Guentert, P.structure solution
CYANA1.0.7Guentert, P.refinement
RefinementMethod: torsion angle dynamic / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
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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