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- PDB-1vb7: Solution structure of the PDZ domain of PDZ and LIM domain 2 -

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Basic information

Entry
Database: PDB / ID: 1vb7
TitleSolution structure of the PDZ domain of PDZ and LIM domain 2
ComponentsPDZ and LIM domain 2
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / PDZ domain PDZ-LIM protein / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


muscle structure development / filamin binding / muscle alpha-actinin binding / cortical actin cytoskeleton / myosin heavy chain binding / alpha-actinin binding / filamentous actin / stress fiber / adherens junction / Z disc ...muscle structure development / filamin binding / muscle alpha-actinin binding / cortical actin cytoskeleton / myosin heavy chain binding / alpha-actinin binding / filamentous actin / stress fiber / adherens junction / Z disc / actin binding / heart development / actin cytoskeleton organization / metal ion binding
Similarity search - Function
Domain of unknown function DUF4749 / Domain of unknown function (DUF4749) / 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 ...Domain of unknown function DUF4749 / Domain of unknown function (DUF4749) / 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 2
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR
AuthorsHatta, R. / Hayashi, F. / Yoshida, M. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Solution structure of the PDZ domain of PDZ and LIM domain 2
Authors: Hatta, R. / Hayashi, F. / Yoshida, M. / Yokoyama, S.
History
DepositionFeb 24, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 30, 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_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 1.4Dec 27, 2023Group: 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: PDZ and LIM domain 2


Theoretical massNumber of molelcules
Total (without water)9,7081
Polymers9,7081
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 least restraint violations, target function
RepresentativeModel #1lowest energy

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Components

#1: Protein PDZ and LIM domain 2


Mass: 9707.788 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: cDNA 2310041E13 / Plasmid: P030203-89 / References: UniProt: Q8R1G6

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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: 1.28mM 13C, 15N-labeled protein; 20mM phosphate buffer; 100mM NaCl; 1mM d10-DTT; 0.02% NaN3; 10% D2O
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 120 / 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 spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 800 MHz

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Processing

NMR software
NameVersionDeveloperClassification
VNMR6.1CVARIANcollection
NMRPipe2002045DELAGLIO, F.processing
NMRView5.0.4Johonson, B. A.data analysis
KUJIRA0.86Kobayashi, N.data analysis
CYANA1.0.7Guentert, P.structure solution
CYANA1.0.7Guentert, P.refinement
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations, target function
Conformers calculated total number: 100 / Conformers submitted total number: 20

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