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- PDB-6sl7: The Delta Calcium mutant of ALPHA-ACTININ FROM ENTAMOEBA HISTOLYTICA -

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Basic information

Entry
Database: PDB / ID: 6sl7
TitleThe Delta Calcium mutant of ALPHA-ACTININ FROM ENTAMOEBA HISTOLYTICA
ComponentsCalponin homology domain protein putative
KeywordsSTRUCTURAL PROTEIN / Actinin / Actin Binding Domain / Spectrin Repear / Calmodulin-like domain / Calcium Regulation
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, calcium binding motif ...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, 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
Similarity search - Domain/homology
Calponin homology domain protein, putative
Similarity search - Component
Biological speciesEntamoeba histolytica (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsPinotsis, N. / Lopez Arolas, A. / Djinovic-Carugo, K.
Funding support Austria, 2items
OrganizationGrant numberCountry
Austrian Science Fund Austria
Marie Sklodowska-Curie Actions, FragNET ITN238423
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2020
Title: Calcium modulates the domain flexibility and function of an alpha-actinin similar to the ancestral alpha-actinin.
Authors: Pinotsis, N. / Zielinska, K. / Babuta, M. / Arolas, J.L. / Kostan, J. / Khan, M.B. / Schreiner, C. / Salmazo, A. / Ciccarelli, L. / Puchinger, M. / Gkougkoulia, E.A. / Ribeiro Jr., E.A. / ...Authors: Pinotsis, N. / Zielinska, K. / Babuta, M. / Arolas, J.L. / Kostan, J. / Khan, M.B. / Schreiner, C. / Salmazo, A. / Ciccarelli, L. / Puchinger, M. / Gkougkoulia, E.A. / Ribeiro Jr., E.A. / Marlovits, T.C. / Bhattacharya, A. / Djinovic-Carugo, K.
History
DepositionAug 18, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 26, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 4, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Calponin homology domain protein putative


Theoretical massNumber of molelcules
Total (without water)69,8541
Polymers69,8541
Non-polymers00
Water00
1
A: Calponin homology domain protein putative

A: Calponin homology domain protein putative


Theoretical massNumber of molelcules
Total (without water)139,7072
Polymers139,7072
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_755-x+2,y,-z+1/21
Buried area7570 Å2
ΔGint-16 kcal/mol
Surface area64720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.739, 75.526, 234.252
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number17
Space group name H-MP2221
Space group name HallP2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2

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Components

#1: Protein Calponin homology domain protein putative / Calponin homology domain protein / putative


Mass: 69853.633 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Entamoeba histolytica (eukaryote) / Gene: CL6EHI_199000, EHI_199000 / Production host: Escherichia coli (E. coli) / References: UniProt: C4LWU6
Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.59 Å3/Da / Density % sol: 52.49 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.1 M bis-tris (pH 5.5), 0.3 M MgCl2, 20% (w/v) PEG 3,350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.96862 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Aug 1, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96862 Å / Relative weight: 1
ReflectionResolution: 3.3→46.85 Å / Num. obs: 11494 / % possible obs: 97.8 % / Redundancy: 4.6 % / CC1/2: 0.998 / Rrim(I) all: 0.084 / Net I/σ(I): 11.57
Reflection shellResolution: 3.3→3.38 Å / Redundancy: 5.8 % / Num. unique obs: 2235 / CC1/2: 0.855 / % possible all: 96.2

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Processing

Software
NameClassification
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6SL2

6sl2


Resolution: 3.3→46.32 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.3081 537 4.7 %
Rwork0.23358 --
obs0.23711 10923 99.04 %
Refinement stepCycle: LAST / Resolution: 3.3→46.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4799 0 0 0 4799

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