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- PDB-5x1x: Solution NMR Structure of DNA Mismatch Repair Protein MutT (Famil... -

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Basic information

Entry
Database: PDB / ID: 5x1x
TitleSolution NMR Structure of DNA Mismatch Repair Protein MutT (Family Nudix Hydrolase) from Methicillin Resistant Staphylococcus aureus 252
ComponentsMutator mutT protein
KeywordsHYDROLASE / divalent ion (Mg2+ / Ca2+) binding protein / adenosine monophosphate (AMP) binding protein
Function / homology
Function and homology information


8-oxo-dGTP diphosphatase / 8-oxo-7,8-dihydrodeoxyguanosine triphosphate pyrophosphatase activity / DNA repair
Similarity search - Function
: / MutY, C-terminal / NUDIX domain / Nucleoside Triphosphate Pyrophosphohydrolase / Nucleoside Triphosphate Pyrophosphohydrolase / NUDIX domain / Nudix hydrolase domain profile. / NUDIX hydrolase domain / NUDIX hydrolase-like domain superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
8-oxo-dGTP diphosphatase
Similarity search - Component
Biological speciesStaphylococcus aureus subsp. aureus MN8 (bacteria)
MethodSOLUTION NMR / distance geometry
AuthorsWahab, A. / Durreshahwar, S. / Schwalbe, H. / Richter, C. / Choudhary, M.I.
CitationJournal: To Be Published
Title: Solution NMR Structure of DNA Mismatch Repair Protein MutT (Family Nudix Hydrolase) from Methicillin Resistant Staphylococcus aureus 252
Authors: Wahab, A.
History
DepositionJan 27, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 22, 2017Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Structure summary
Category: database_2 / entity ...database_2 / entity / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_number_of_molecules / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
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

Downloads & links

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Assembly

Deposited unit
A: Mutator mutT protein


Theoretical massNumber of molelcules
Total (without water)14,9141
Polymers14,9141
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area8030 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100all calculated structures submitted
RepresentativeModel #1lowest energy

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Components

#1: Protein Mutator mutT protein


Mass: 14914.342 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: methicillin resistant
Source: (gene. exp.) Staphylococcus aureus subsp. aureus MN8 (bacteria)
Cell: Bacterial / Gene: HMPREF0769_10658 / Variant: MRSA252 / Plasmid: pSpeedET
Details (production host): Bacterial expression vector, arabinose or T7 induced expression, adds N-terminal MGSDKIHHHHHHENLYFQG tag; kanamycin resistance; PIPE cloning
Cell (production host): bacterial / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A0E1XLJ5, 8-oxo-dGTP diphosphatase

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N HSQC
121isotropic13D HNCO
131isotropic13D HNCA
141isotropic13D HN(CA)CB
181isotropic13D HNHA
1101isotropic23D CC(CO)NH
191isotropic23D (H)CC(CO)NH
151isotropic13D 1H-15N NOESY
161isotropic13D 1H-13C NOESY aliphatic
171anisotropic13D 1H-13C NOESY aromatic

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Sample preparation

DetailsType: solution
Contents: 1 mM [U-99% 13C; U-99% 15N] DNA Mismatch Repair Protein MutT from Nudix Hydrolase Family, 95% H2O/5% D2O
Details: The protein sample was made using 25 mM sodium phosphate buffer, pH 6.9, 100 mM NaCl, 1 mM DTT, 0.15 mM DSS, 5% D2O
Label: 15N, 13C labeled / Solvent system: 95% H2O/5% D2O
SampleConc.: 1 mM
Component: DNA Mismatch Repair Protein MutT from Nudix Hydrolase Family
Isotopic labeling: [U-99% 13C; U-99% 15N]
Sample conditionsDetails: The protein sample was made using 25 mM sodium phosphate buffer, pH 6.9, 100 mM NaCl, 1 mM DTT, 0.15 mM DSS, 5% D2O
Ionic strength: 25 mM sodium phosphate, 100 mM NaCl mM / Label: conditions-1 / pH: 6.9 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-IDDetails
Bruker AscendBrukerAscend8001Equipped with cryogenically cooled probe
Bruker AVANCE IIIBrukerAVANCE III6002Equipped with cryogenically cooled probe

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin3.6 pl5Bruker Biospincollection
TopSpin3.5 pl5Bruker Biospinprocessing
CARAKeller and Wuthrichdata analysis
SparkySPARKY 3T. D. Goddard and D. G. Knellerdata analysis
CARAKeller and Wuthrichchemical shift assignment
SparkySPARKY 3T. D. Goddard and D. G. Knellerchemical shift assignment
CYANA3.97Guntert, Mumenthaler and Wuthrichstructure calculation
CYANA3.97Guntert, Mumenthaler and Wuthrichrefinement
RefinementMethod: distance geometry / Software ordinal: 8
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: all calculated structures submitted
Conformers calculated total number: 100 / Conformers submitted total number: 20

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