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- PDB-2m7l: Alfa-actinin from parasite Entamoeba histolytica -

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Basic information

Entry
Database: PDB / ID: 2m7l
TitleAlfa-actinin from parasite Entamoeba histolytica
ComponentsCalponin homology domain protein, putative
KeywordsSTRUCTURAL PROTEIN
Function / homology
Function and homology information


actin binding / calcium ion binding
Similarity search - Function
Ca2+ insensitive EF hand / Actinin-type actin-binding domain signature 1. / Actinin-type actin-binding domain signature 2. / Actinin-type actin-binding domain, conserved site / Calponin homology domain / Calponin homology (CH) domain / Calponin homology domain / CH domain superfamily / Calponin homology (CH) domain profile. / EF-hand ...Ca2+ insensitive EF hand / Actinin-type actin-binding domain signature 1. / Actinin-type actin-binding domain signature 2. / Actinin-type actin-binding domain, conserved site / Calponin homology domain / Calponin homology (CH) domain / Calponin homology domain / CH domain superfamily / Calponin homology (CH) domain profile. / EF-hand / Recoverin; domain 1 / 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
Calponin homology domain protein, putative
Similarity search - Component
Biological speciesEntamoeba histolytica (eukaryote)
MethodSOLUTION NMR / molecular dynamics
Model detailslowest energy, model1
AuthorsPersson, C.K. / Mayzel, M.L. / Karlsson, B.G. / Backman, L.
CitationJournal: To be Published
Title: Alfa-actinin from parasite Entamoeba histolytica
Authors: Persson, C.K. / Mayzel, M.L. / Karlsson, B.G. / Backman, L.
History
DepositionApr 26, 2013Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Jun 5, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2013Group: Structure summary
Revision 1.2Jun 14, 2023Group: Database references / Other
Category: database_2 / pdbx_database_status / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Calponin homology domain protein, putative


Theoretical massNumber of molelcules
Total (without water)15,9241
Polymers15,9241
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)12 / 100target function
RepresentativeModel #1lowest energy

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Components

#1: Protein Calponin homology domain protein, putative /


Mass: 15924.232 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Entamoeba histolytica (eukaryote) / Gene: EHI_199000 / Production host: Escherichia coli (E. coli) / References: UniProt: C4LWU6

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC/HMQC
1213D 1H-15N NOESY
1313D 1H-13C NOESY
1412D 1H-1H NOESY

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Sample preparation

DetailsContents: 1.5 mM [U-100% 13C; U-100% 15N] The protein-1, 25 mM sodium phosphate-2, 150 mM sodium chloride-3, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.5 mMThe protein-1[U-100% 13C; U-100% 15N]1
25 mMsodium phosphate-21
150 mMsodium chloride-31
Sample conditionsIonic strength: 0.15 / pH: 6.0 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA8001
Varian INOVAVarianINOVA9002

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Processing

NMR software
NameVersionDeveloperClassification
CYANA2.2Guntert, Mumenthaler and Wuthrichstructure solution
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: molecular dynamics / Software ordinal: 1
Details: The ensemble was refined using CNS water refinement
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 12 / Representative conformer: 1

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