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- PDB-2m2l: Solution structure of Entamoeba histolytica HP1 chromodomain -

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Basic information

Entry
Database: PDB / ID: 2m2l
TitleSolution structure of Entamoeba histolytica HP1 chromodomain
ComponentsPutative uncharacterized protein
KeywordsNUCLEAR PROTEIN / chromodomain / HP1 / Entamoeba histolytica
Function / homology
Function and homology information


Chromo domain, conserved site / Chromo domain signature. / Chromo domain / Chromo (CHRromatin Organisation MOdifier) domain / Chromo and chromo shadow domain profile. / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #40 / Chromo/chromo shadow domain / Chromatin organization modifier domain / Chromo-like domain superfamily / OB fold (Dihydrolipoamide Acetyltransferase, E2P) ...Chromo domain, conserved site / Chromo domain signature. / Chromo domain / Chromo (CHRromatin Organisation MOdifier) domain / Chromo and chromo shadow domain profile. / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #40 / Chromo/chromo shadow domain / Chromatin organization modifier domain / Chromo-like domain superfamily / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Uncharacterized protein
Similarity search - Component
Biological speciesEntamoeba histolytica (eukaryote)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 1
AuthorsWiggins, K.R. / Ren, X. / Ali, I.K.M. / Petri, W.A. / Khorasanizadeh, S.
CitationJournal: To be Published
Title: Characterization of putative readers of epigenetic methyl-marks from Entamoeba histolytica
Authors: Ali, I. / Wiggins, K.R. / Ren, X. / Sherman, N. / Petri, W. / Khorasanizadeh, S.
History
DepositionDec 28, 2012Deposition site: BMRB / Processing site: RCSB
Revision 1.0May 14, 2014Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / 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 / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.2May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)8,2231
Polymers8,2231
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Putative uncharacterized protein


Mass: 8223.149 Da / Num. of mol.: 1 / Fragment: Entamoeba histolytica HP1 chromodomain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Entamoeba histolytica (eukaryote) / Gene: EHI_200710 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus (DE3) / References: UniProt: C4M3X7

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1222D 1H-13C HSQC
1323D CBCA(CO)NH
1423D HN(CA)CB
1523D HNCO
1623D (H)CCH-TOCSY
1723D 1H-15N NOESY
1823D 1H-13C NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
150 mM sodium phosphate, 25 mM sodium chloride, 1 mM DTT, 5 % [U-100% 2H] D2O, 95% H2O/5% D2O95% H2O/5% D2O
250 mM sodium phosphate, 25 mM sodium chloride, 1 mM DTT, 5 % [U-100% 2H] D2O, 95% H2O/5% D2O95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
50 mMsodium phosphate-11
25 mMsodium chloride-21
1 mMDTT-31
5 %D2O-4[U-100% 2H]1
50 mMsodium phosphate-52
25 mMsodium chloride-62
1 mMDTT-72
5 %D2O-8[U-100% 2H]2
Sample conditionsIonic strength: 75 / pH: 6.0 / Pressure: ambient / Temperature: 293 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz

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Processing

NMR software
NameDeveloperClassification
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRViewJohnson, One Moon Scientificchemical shift assignment
NMRViewJohnson, One Moon Scientificdata analysis
NMRViewJohnson, One Moon Scientificpeak picking
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
TopSpinBruker Biospincollection
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
CYANAGuntert, Mumenthaler and Wuthrichrefinement
CYANAGuntert, Mumenthaler and Wuthrichdata analysis
TALOSCornilescu, Delaglio and Baxdata analysis
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20

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