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- PDB-2mhc: NMR structure of the catalytic domain of the large serine resolva... -

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Basic information

Entry
Database: PDB / ID: 2mhc
TitleNMR structure of the catalytic domain of the large serine resolvase TnpX
ComponentsTnpX
KeywordsRECOMBINATION / SERINE RESOLVASE
Function / homology
Function and homology information


DNA strand exchange activity / DNA binding
Similarity search - Function
Domain of unknown function DUF4368 / Domain of unknown function (DUF4368) / Recombinase zinc beta ribbon domain / Recombinase / Recombinase zinc beta ribbon domain / DNA-binding recombinase domain / DNA-binding recombinase domain superfamily / DNA-binding recombinase domain profile. / Resolvase, N-terminal catalytic domain / Resolvase/invertase-type recombinase catalytic domain profile. ...Domain of unknown function DUF4368 / Domain of unknown function (DUF4368) / Recombinase zinc beta ribbon domain / Recombinase / Recombinase zinc beta ribbon domain / DNA-binding recombinase domain / DNA-binding recombinase domain superfamily / DNA-binding recombinase domain profile. / Resolvase, N-terminal catalytic domain / Resolvase/invertase-type recombinase catalytic domain profile. / Resolvase, N-terminal catalytic domain / Resolvase-like, N-terminal catalytic domain superfamily / Resolvase, N terminal domain / Resolvase, N terminal domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesClostridium perfringens (bacteria)
MethodSOLUTION NMR / TORSION ANGLE DYNAMICS, SIMULATED ANNEALING, SIMULATED ANNEALING
Model detailslowest energy, model1
AuthorsHeadey, S.J. / Sivakumaran, A. / Adams, V. / Rodgers, A.J.W. / Rood, J.I. / Scanlon, M.J. / Wilce, M.C.J.
CitationJournal: To be Published
Title: Solution Structure and DNA Binding of the Catalytic of the Large Serine Resolvase Tnpx
Authors: Headey, S.J. / Sivakumaran, A. / Adams, V. / Rodgers, A.J.W. / Scanlon, J.I. / Wilce, M.C.J.
History
DepositionNov 20, 2013Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Nov 26, 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 / 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 / _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: TnpX


Theoretical massNumber of molelcules
Total (without water)13,7931
Polymers13,7931
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)10 / 100STRUCTURES WITH THE LOWEST ENER
RepresentativeModel #1lowest energy

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Components

#1: Protein TnpX


Mass: 13793.226 Da / Num. of mol.: 1 / Fragment: UNP residues 2-120
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium perfringens (bacteria) / Gene: TN4451, tnpX / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): C43 / References: UniProt: O05415

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1313D HN(CA)CB
1413D HNCO
1513D HN(CA)CO 3D CBCA(CO)NH
1613D H(CCO)NH
1713D H(CCO)NH
1813D (H)CCH-TOCSY
1912D (HB)CB(CGCD)HD
11013D (H)CCH-TOCSY 2D (HB)CB(CGCDCE)HE
11113D 1H-15N NOESY
11213D 1H-13C NOESY
11312D 1H-1 NOESY
11412D 1H-15N NOE

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Sample preparation

DetailsContents: 0.4mM [U-99% 13C; U-99% 15N] TNPX-1, 10% D2O-2, 150mM sodium chloride-3, 20mM sodium phosphate-4, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.4 mMTNPX-1[U-99% 13C; U-99% 15N]1
10 %D2O-21
150 mMsodium chloride-31
20 mMsodium phosphate-41
Sample conditionsIonic strength: 150 / pH: 7.0 / Temperature: 298 K

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NMR measurement

NMR spectrometerType: VARIAN INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CNSSOLVE1.2BRUNGER, ADAMS, CLORE, GROS, NILGESrefinement
XEASY1.4Bartels et al.structure solution
TopSpinBruker Biospinprocessing
VnmrJVariancollection
RefinementMethod: TORSION ANGLE DYNAMICS, SIMULATED ANNEALING, SIMULATED ANNEALING
Software ordinal: 1
Details: FROM EXTENDED CONFORMER, FROM FOLDED CONFORMER, IN TIP3 WATER
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: STRUCTURES WITH THE LOWEST ENER
Conformers calculated total number: 100 / Conformers submitted total number: 10 / Representative conformer: 1

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