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- PDB-1q27: NMR Solution Structure of DR0079: An hypothetical Nudix protein f... -

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Basic information

Entry
Database: PDB / ID: 1q27
TitleNMR Solution Structure of DR0079: An hypothetical Nudix protein from D. radiodurans
ComponentsPutative Nudix hydrolase DR0079
KeywordsHYDROLASE / Nudix hydrolase / radiation resistance
Function / homology
Function and homology information


nucleotide metabolic process / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / hydrolase activity / nucleotide binding / magnesium ion binding
Similarity search - Function
Nucleoside Triphosphate Pyrophosphohydrolase / Nucleoside Triphosphate Pyrophosphohydrolase / NUDIX hydrolase, conserved site / Nudix box signature. / NUDIX domain / Nudix hydrolase domain profile. / NUDIX hydrolase domain / NUDIX hydrolase-like domain superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Nudix hydrolase DR_0079
Similarity search - Component
Biological speciesDeinococcus radiodurans (radioresistant)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsBuchko, G.W. / Ni, S. / Holbrook, S.R. / Kennedy, M.A.
Citation
Journal: Proteins / Year: 2004
Title: Solution structure of hypothetical Nudix hydrolase DR0079 from extremely radiation-resistant Deinococcus radiodurans bacterium
Authors: Buchko, G.W. / Ni, S. / Holbrook, S.R. / Kennedy, M.A.
#1: Journal: J.Biomol.NMR / Year: 2003
Title: 1H, 13C and 15N NMR assignments of the hypothetical Nudix protein DR0079 from the extremely radiation-resistant bacterium Deinococcus radiodurans
Authors: Buchko, G.W. / Ni, S. / Holbrook, S.A. / Kennedy, M.A.
History
DepositionJul 23, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 12, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative Nudix hydrolase DR0079


Theoretical massNumber of molelcules
Total (without water)19,3041
Polymers19,3041
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 / 225ten best structures, in terms of total and NOE energies
RepresentativeModel #6

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Components

#1: Protein Putative Nudix hydrolase DR0079 / MutT/nudix family protein


Mass: 19303.561 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Deinococcus radiodurans (radioresistant)
Gene: DR0079 / Plasmid: pET30b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9RY71

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
1213D 13C-separated NOESY
1314D 13C-separated NOESY
242IPAP-HSQC experiements for RDCs

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Sample preparation

Details
Solution-IDContentsSolvent system
1~2 mM DR0079; U-15N, 13C; 100 mM KCl, 20 mM potassium phosphate, 2 mM DTT, pH 7.190% H2O/10% D2O
2~2 mM DR0079; U-15N, 13C; 100 mM KCl, 20 mM potassium phosphate, 2 mM DTT, pH 7.1, pf1 filamentous phage90% H2O/10% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
1100 mM KCl; 20 mM Potassium phosphate 7.1ambient 298 K
2100 mM KCl; 20 mM Potassium phosphate 7.1ambient 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA7501
Varian INOVAVarianINOVA8002
Varian INOVAVarianINOVA6003

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Processing

NMR software
NameVersionDeveloperClassification
DYANA1.5Guentertstructure solution
CNS1.1Brungerstructure solution
Felix97MSIprocessing
CNS1.1Brungerrefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
Details: DYANA used for initial refinements. CNS used for final structure calculations with RDCs.
NMR ensembleConformer selection criteria: ten best structures, in terms of total and NOE energies
Conformers calculated total number: 225 / Conformers submitted total number: 10

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