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- PDB-2cvr: NMR solution structure of sso7d mutant, K12L, 12 conformers -

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Basic information

Entry
Database: PDB / ID: 2cvr
TitleNMR solution structure of sso7d mutant, K12L, 12 conformers
ComponentsDNA-binding protein 7a
KeywordsDNA BINDING PROTEIN / DNA-binding protein / thermostable protein / Sulfolobus solfataricus / single point mutation
Function / homology
Function and homology information


Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters / RNA endonuclease activity / DNA binding
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 7a
Similarity search - Component
Biological speciesSulfolobus solfataricus (archaea)
MethodSOLUTION NMR / simulated annealing
Model type detailsminimized average
AuthorsArosio, I. / Recca, T. / Consonni, R. / Alberti, E. / Fusi, P. / Zetta, L.
Citation
Journal: To be Published
Title: Structural Determinants Responsible for the Thermostability of Sso7d and its Single Point Mutants
Authors: Arosio, I. / Recca, T. / Consonni, R. / Alberti, E. / Fusi, P. / Zetta, L.
#1: Journal: Biochemistry / Year: 1999
Title: A single-point mutation in the extreme heat- and pressure-resistant sso7d protein from sulfolobus solfataricus leads to a major rearrangement of the hydrophobic core
Authors: Consonni, R. / Santomo, L. / Fusi, P. / Tortora, P. / Zetta, L.
#2: Journal: Biochemistry / Year: 2003
Title: Investigations of Sso7d catalytic residues by NMR titration shifts and electrostatic calculations
Authors: Consonni, R. / Arosio, I. / Belloni, B. / Fogolari, F. / Fusi, P. / Shehi, E. / Zetta, L.
History
DepositionJun 13, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 29, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
SupersessionApr 4, 2012ID: 1R83
Revision 1.3Apr 4, 2012Group: Other
Revision 1.4Nov 10, 2021Group: Data collection / Database references
Category: database_2 / 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_nmr_software.name / _struct_ref_seq_dif.details
Revision 1.5May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Remark 650HELIX DETERMINATION METHOD: AUTHOR DETERMINED
Remark 700SHEET DETERMINATION METHOD: AUTHOR DETERMINED

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA-binding protein 7a


Theoretical massNumber of molelcules
Total (without water)7,0181
Polymers7,0181
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)12 / 50structures with the least restraint violations
RepresentativeModel #1minimized average structure

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Components

#1: Protein DNA-binding protein 7a / sso7d / 7 kDa DNA-binding protein a / Endoribonuclease P2 / p7ss


Mass: 7018.202 Da / Num. of mol.: 1 / Mutation: K12L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus solfataricus (archaea) / Plasmid: PT7-7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) PLYSE
References: UniProt: P61991, Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters

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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

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Sample preparation

Details
Solution-IDContentsSolvent system
12mM K12L; 90% H2O, 10% D2O90% H2O/10% D2O
22mM K12L; 100% D2O100% D2O
Sample conditionspH: 4.5 / Pressure: AMBIENT / Temperature: 300 K

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NMR measurement

NMR spectrometerType: Bruker DMX / Manufacturer: Bruker / Model: DMX / Field strength: 500 MHz

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Processing

NMR software
NameVersionDeveloperClassification
Discover3DAUBER-OSGUTHORPErefinement
Felix98msidata analysis
Discover3msistructure solution
XwinNMR2.6Brukerstructure solution
RefinementMethod: simulated annealing / Software ordinal: 1
Details: The structures are based on a total of 683 restraints, 660 are noe-derived distance constraints, 7 dihedral angle restraints, 16 distance restraints from hydrogen bonds.
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 50 / Conformers submitted total number: 12

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