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- PDB-1la3: Solution structure of recoverin mutant, E85Q -

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Basic information

Entry
Database: PDB / ID: 1la3
TitleSolution structure of recoverin mutant, E85Q
ComponentsRecoverin
KeywordsMETAL BINDING PROTEIN / EF-hand / calcium / vision / E85Q / Metal-binding protein
Function / homology
Function and homology information


Inactivation, recovery and regulation of the phototransduction cascade / regulation of calcium ion transport / phototransduction / photoreceptor outer segment / photoreceptor inner segment / visual perception / perikaryon / calcium ion binding / membrane / cytosol
Similarity search - Function
Recoverin family / EF hand / EF-hand domain pair / EF-hand / Recoverin; domain 1 / EF-hand domain pair / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. ...Recoverin family / EF hand / EF-hand domain pair / EF-hand / Recoverin; domain 1 / EF-hand domain pair / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
MYRISTIC ACID / Recoverin
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodSOLUTION NMR / distance geometry, simulated annealing
AuthorsAmes, J.B. / Hamasaki, N. / Molchanova, T.
CitationJournal: Biochemistry / Year: 2002
Title: Structure and calcium-binding studies of a recoverin mutant (E85Q) in an allosteric intermediate state.
Authors: Ames, J.B. / Hamasaki, N. / Molchanova, T.
History
DepositionMar 27, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 19, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Derived calculations / Structure summary
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_oper_list / struct_conn / struct_keywords / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_keywords.text / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 30, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Remark 999 SEQUENCE Methionine 1 is removed from the protein during myristoylation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Recoverin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,5033
Polymers23,2341
Non-polymers2682
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)14 / 20The submitted conformer models are the 14 structures with lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Recoverin


Mass: 23234.223 Da / Num. of mol.: 1 / Mutation: E85Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Tissue: retina / Plasmid: pTREC2 / Production host: Escherichia coli (E. coli) / Strain (production host): DH5A / References: UniProt: P21457
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-MYR / MYRISTIC ACID


Mass: 228.371 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H28O2
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
1213D 13C-separated NOESY
131HNHA
NMR detailsText: The structure was determined using standard triple-resonance NMR spectroscopy

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Sample preparation

DetailsContents: 0.8mM recoverin-E85Q U-15N,13C; 10 mM imidazole, 50mM KCl, 1 mM CaCl2, 10 mM dithiothreitol, 1mM MgCl2, pH 6.7; 95% H2O, 5% D2O
Solvent system: 95% H2O/5% D2O
Sample conditionsIonic strength: 50 mM / pH: 6.7 / Pressure: ambient / Temperature: 310 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR3.1Brungerstructure solution
NMRPipe2.1Delaglioprocessing
X-PLOR3.1Brungerrefinement
RefinementMethod: distance geometry, simulated annealing / Software ordinal: 1
Details: The structures are based on a total of 2050 NOE-derived distance constraints, 230 dihedral angle restraints, and 150 distance restraints from hydrogen bonds.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: The submitted conformer models are the 14 structures with lowest energy
Conformers calculated total number: 20 / Conformers submitted total number: 14

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