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- PDB-6sl3: ALPHA-ACTININ FROM ENTAMOEBA HISTOLYTICA in orthorhombic space group -

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Basic information

Entry
Database: PDB / ID: 6sl3
TitleALPHA-ACTININ FROM ENTAMOEBA HISTOLYTICA in orthorhombic space group
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
Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #60 / Calponin-like domain / Actin-binding Protein, T-fimbrin; domain 1 / 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 ...Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #60 / Calponin-like domain / Actin-binding Protein, T-fimbrin; domain 1 / 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 / Methane Monooxygenase Hydroxylase; Chain G, 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 / Up-down Bundle / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Calponin homology domain protein, putative
Similarity search - Component
Biological speciesEntamoeba histolytica (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsPinotsis, N. / Khan, M.B. / 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

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Assembly

Deposited unit
A: Calponin homology domain protein putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,8122
Polymers69,7721
Non-polymers401
Water00
1
A: Calponin homology domain protein putative
hetero molecules

A: Calponin homology domain protein putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)139,6234
Polymers139,5432
Non-polymers802
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Buried area8880 Å2
ΔGint-24 kcal/mol
Surface area62680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.210, 71.830, 241.680
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: 69771.500 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
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

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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: 2.69 Å3/Da / Density % sol: 54.24 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 92 mM bicine/trizma base (pH 8.5), 27.6 mM CaCl2, 27.6 mM MgCl2, 11.5% (w/v) PEG 3,350, 11.5% (w/v) PEG 1,000, 11.5% (v/v) MPD

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.005755 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 1, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.005755 Å / Relative weight: 1
ReflectionResolution: 3.1→46.24 Å / Num. obs: 14460 / % possible obs: 99.1 % / Redundancy: 7 % / CC1/2: 0.99 / Rmerge(I) obs: 0.133 / Net I/σ(I): 8.57
Reflection shellResolution: 3.1→3.17 Å / Mean I/σ(I) obs: 0.48 / Num. unique obs: 967 / CC1/2: 0.433

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Processing

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

6sl2


Resolution: 3.1→46.23 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.32451 --
Rwork0.25907 --
obs0.26829 12224 99.08 %
Refinement stepCycle: LAST / Resolution: 3.1→46.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4730 0 1 0 4731

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