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- PDB-2l8l: Structure of an engineered splicing intein mutant based on Mycoba... -

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Basic information

Entry
Database: PDB / ID: 2l8l
TitleStructure of an engineered splicing intein mutant based on Mycobacterium tuberculosis RecA
ComponentsEndonuclease PI-MtuI
KeywordsHYDROLASE
Function / homology
Function and homology information


UV protection / DNA strand invasion / intein-mediated protein splicing / intron homing / DNA strand exchange activity / recombinational repair / ATP-dependent DNA damage sensor activity / SOS response / ATP-dependent activity, acting on DNA / DNA endonuclease activity ...UV protection / DNA strand invasion / intein-mediated protein splicing / intron homing / DNA strand exchange activity / recombinational repair / ATP-dependent DNA damage sensor activity / SOS response / ATP-dependent activity, acting on DNA / DNA endonuclease activity / single-stranded DNA binding / manganese ion binding / endonuclease activity / damaged DNA binding / Hydrolases; Acting on ester bonds / response to antibiotic / DNA repair / DNA damage response / magnesium ion binding / ATP hydrolysis activity / ATP binding / cytoplasm / cytosol
Similarity search - Function
Endonuclease - Pi-scei; Chain A, domain 1 / Hedgehog/Intein (Hint) domain / LAGLIDADG-like domain / : / : / RecA C-terminal domain / DNA recombination/repair protein RecA, conserved site / DNA recombination and repair protein RecA, C-terminal / recA signature. / DNA recombination and repair protein RecA ...Endonuclease - Pi-scei; Chain A, domain 1 / Hedgehog/Intein (Hint) domain / LAGLIDADG-like domain / : / : / RecA C-terminal domain / DNA recombination/repair protein RecA, conserved site / DNA recombination and repair protein RecA, C-terminal / recA signature. / DNA recombination and repair protein RecA / recA bacterial DNA recombination protein / Intein splicing domain / Intein / Intein DOD homing endonuclease / Intein DOD-type homing endonuclease domain profile. / Homing endonuclease, LAGLIDADG / Intein C-terminal splicing region / Intein C-terminal splicing motif profile. / Hint domain C-terminal / Hint (Hedgehog/Intein) domain C-terminal region / Intein N-terminal splicing region / Intein N-terminal splicing motif profile. / Hint domain N-terminal / Hint (Hedgehog/Intein) domain N-terminal region / Homing endonuclease / Hint domain superfamily / DNA recombination and repair protein RecA, monomer-monomer interface / RecA family profile 2. / DNA recombination and repair protein RecA-like, ATP-binding domain / RecA family profile 1. / Beta Complex / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta
Similarity search - Domain/homology
Protein RecA / Protein RecA
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 2
AuthorsDu, Z. / Wang, C.
CitationJournal: J.Am.Chem.Soc. / Year: 2011
Title: pK(a) coupling at the intein active site: implications for the coordination mechanism of protein splicing with a conserved aspartate.
Authors: Du, Z. / Zheng, Y. / Patterson, M. / Liu, Y. / Wang, C.
History
DepositionJan 19, 2011Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jan 4, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 6, 2021Group: Data collection / Database references
Category: database_2 / pdbx_nmr_software / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _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: Endonuclease PI-MtuI


Theoretical massNumber of molelcules
Total (without water)15,4241
Polymers15,4241
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 Endonuclease PI-MtuI / Mtu recA intein


Mass: 15423.512 Da / Num. of mol.: 1 / Fragment: sequence database residues 252-345, 654-691
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: MT2806, MTV002.02c, recA, Rv2737c / Production host: Escherichia coli (E. coli)
References: UniProt: P0A5U4, UniProt: P9WHJ3*PLUS, Hydrolases; Acting on ester bonds

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D (H)CCH-COSY
1213D HN(CA)CB
1313D 1H-13C NOESY aliphatic

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Sample preparation

DetailsContents: 50 mM sodium phosphate, 100 mM sodium chloride, 1 mM sodium azide, 0.15-0.2 mM [U-98% 13C; U-98% 15N] protein, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)UnitsComponentIsotopic labelingConc. range (mg/ml)Solution-ID
50 mMsodium phosphate-11
100 mMsodium chloride-21
1 mMsodium azide-31
mMprotein-4[U-98% 13C; U-98% 15N]0.15-0.21
Sample conditionsIonic strength: 150 / pH: 7 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker ARXBrukerARX8001
Bruker ARXBrukerARX6002

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Processing

NMR software
NameDeveloperClassification
SparkyGoddardchemical shift assignment
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure solution
X-PLOR NIHrefinement
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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