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- PDB-1xx8: NMR Structure of the W24A Mutant of the Hyperthermophile Sac7d Protein -

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Basic information

Entry
Database: PDB / ID: 1xx8
TitleNMR Structure of the W24A Mutant of the Hyperthermophile Sac7d Protein
ComponentsSac7d
KeywordsDNA BINDING PROTEIN / hyperthermophile / DNA-binding protein
Function / homology
Function and homology information


RNA endonuclease activity / DNA binding / cytoplasm
Similarity search - Function
DNA-binding 7kDa protein / 7kD DNA-binding domain / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #40 / Chromo-like domain superfamily / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
DNA-binding protein 7d
Similarity search - Component
Biological speciesSulfolobus acidocaldarius (acidophilic)
MethodSOLUTION NMR / Simulated annealing using cartesion, torsion angle dynamics
Model type detailsminimized average
AuthorsBedell, J.L. / Edmondson, S.P. / Shriver, J.W.
CitationJournal: Biochemistry / Year: 2005
Title: Role of a surface tryptophan in defining the structure, stability, and DNA binding of the hyperthermophile protein sac7d
Authors: Bedell, J.L. / Edmondson, S.P. / Shriver, J.W.
History
DepositionNov 4, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 8, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 20, 2021Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / 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 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: Sac7d


Theoretical massNumber of molelcules
Total (without water)7,5121
Polymers7,5121
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)11 / 100structures with the least restraint violations
RepresentativeModel #1minimized average structure

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Components

#1: Protein Sac7d


Mass: 7511.782 Da / Num. of mol.: 1 / Mutation: W24A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus acidocaldarius (acidophilic)
Gene: sac7d / Plasmid: pETBlue-2 / Production host: Escherichia coli (E. coli) / Strain (production host): ResettaBlue(DE3)pLacI (Novagen) / References: UniProt: P13123

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111DQF-COSY
1212D TOCSY
1312D NOESY
141HNHA
1512D HSQC IPAP
NMR detailsText: THIS ENTRY CONSISTS OF 11 MODELS, INCLUDING ONE ENERGY-MINIMIZED AVERAGE STRUCTURE FOLLOWED BY AN ENSEMBLE OF THE 10 BEST NMR STRUCTURES.

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Sample preparation

DetailsContents: 5 mM Sac7d, 90% H2O, 10% D2O / Solvent system: 90% H2O/10% D2O
Sample conditionspH: 4.5 / Pressure: ambient / Temperature: 303 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 500 MHz

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Processing

NMR software
NameVersionDeveloperClassification
VNMR6.1CVariancollection
Felix2000BioSymprocessing
NMRView5.2.2Johnsondata analysis
ARIA1.2Linge, Nilgesstructure solution
CNS1.1Brunger, Clorerefinement
RefinementMethod: Simulated annealing using cartesion, torsion angle dynamics
Software ordinal: 1
Details: NOE assignments, distance restraint calibration, and initial structures were made using ARIA 1.2 with 370 NOE volumes. Final structure refinement was done using CNS 1.1 with 262 unambiguous ...Details: NOE assignments, distance restraint calibration, and initial structures were made using ARIA 1.2 with 370 NOE volumes. Final structure refinement was done using CNS 1.1 with 262 unambiguous distance restraints, 13 H-bonds, 48 HNHA coupling constants, and 59 NH residual dipolar couplings.
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 11

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