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- PDB-2lcj: Solution NMR structure of Pab PolII Intein -

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Basic information

Entry
Database: PDB / ID: 2lcj
TitleSolution NMR structure of Pab PolII Intein
ComponentsPab polC intein
KeywordsHYDROLASE
Function / homology
Function and homology information


exodeoxyribonuclease I / intein-mediated protein splicing / single-stranded DNA 3'-5' DNA exonuclease activity / DNA catabolic process / DNA-templated DNA replication / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / DNA binding
Similarity search - Function
DNA polymerase II large subunit DP2 / DNA polymerase II large subunit DP2, N-terminal / : / : / DNA polymerase II large subunit DP2, N-terminal / DNA polymerase II large subunit DP2, central domain / DNA polymerase II large subunit DP2, catalytic domain / Endonuclease - Pi-scei; Chain A, domain 1 / Hedgehog/Intein (Hint) domain / Intein splicing domain ...DNA polymerase II large subunit DP2 / DNA polymerase II large subunit DP2, N-terminal / : / : / DNA polymerase II large subunit DP2, N-terminal / DNA polymerase II large subunit DP2, central domain / DNA polymerase II large subunit DP2, catalytic domain / Endonuclease - Pi-scei; Chain A, domain 1 / Hedgehog/Intein (Hint) domain / Intein splicing domain / Intein C-terminal splicing region / Intein C-terminal splicing motif profile. / Intein N-terminal splicing region / Intein N-terminal splicing motif profile. / Hint domain N-terminal / Hint (Hedgehog/Intein) domain N-terminal region / Hint domain superfamily / Beta Complex / Mainly Beta
Similarity search - Domain/homology
DNA polymerase II large subunit
Similarity search - Component
Biological speciesPyrococcus abyssi (archaea)
MethodSOLUTION NMR / simulated annealing, torsion angle dynamics
Model detailsclosest to the average, model 1
AuthorsJiajing, L. / Mills, K.V. / Albracht, C.D.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Structural and Mutational Studies of a Hyperthermophilic Intein from DNA Polymerase II of Pyrococcus abyssi.
Authors: Du, Z. / Liu, J. / Albracht, C.D. / Hsu, A. / Chen, W. / Marieni, M.D. / Colelli, K.M. / Williams, J.E. / Reitter, J.N. / Mills, K.V. / Wang, C.
History
DepositionApr 29, 2011Deposition site: BMRB / Processing site: RCSB
Revision 1.0Sep 21, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 16, 2011Group: Database references
Revision 1.2Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status / pdbx_nmr_software
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
Revision 1.3May 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: Pab polC intein


Theoretical massNumber of molelcules
Total (without water)21,5531
Polymers21,5531
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 #1closest to the average

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Components

#1: Protein Pab polC intein / Pab pol II intein


Mass: 21553.291 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus abyssi (archaea) / Strain: GE5 / Orsay / Gene: polC, PYRAB01200, PAB2404 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9V2F4, DNA-directed DNA polymerase

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experimentType: 3D 1H-13C NOESY aliphatic

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Sample preparation

DetailsContents: 2 mM [U-100% 13C; U-100% 15N] protein, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
SampleConc.: 2 mM / Component: protein-1 / Isotopic labeling: [U-100% 13C; U-100% 15N]
Sample conditionsIonic strength: 20 / pH: 6.5 / Pressure: ambient / Temperature: 320 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AMXBrukerAMX8001
Bruker AMXBrukerAMX6002

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Processing

NMR software
NameVersionDeveloperClassification
CYANA3Guntert, Mumenthaler and Wuthrichgeometry optimization
CYANA3Guntert, Mumenthaler and Wuthrichrefinement
X-PLOR NIH2.27Schwieters, Kuszewski, Tjandra and Clorerefinement
X-PLOR NIH2.27Schwieters, Kuszewski, Tjandra and Clorestructure solution
RefinementMethod: simulated annealing, torsion angle dynamics / Software ordinal: 1
Details: xplor refinement with explicit water for final structure, structure model build.
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20

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