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- PDB-2wqg: SAP domain from Tho1: L31W (fluorophore) mutant -

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Basic information

Entry
Database: PDB / ID: 2wqg
TitleSAP domain from Tho1: L31W (fluorophore) mutant
ComponentsPROTEIN THO1
KeywordsUNKNOWN FUNCTION
Function / homology
Function and homology information


poly(A)+ mRNA export from nucleus / protein-RNA complex assembly / transcription elongation by RNA polymerase II / double-stranded DNA binding / chromatin binding / RNA binding / nucleus
Similarity search - Function
THO1_MOS11, C-terminal domain / Tho1/MOS11 C-terminal domain / : / SAP domain / Transcription Termination Factor Rho, Rna-binding Domain; Chain A, Domain 1 / SAP domain superfamily / SAP domain / SAP motif profile. / Putative DNA-binding (bihelical) motif predicted to be involved in chromosomal organisation / SAP domain ...THO1_MOS11, C-terminal domain / Tho1/MOS11 C-terminal domain / : / SAP domain / Transcription Termination Factor Rho, Rna-binding Domain; Chain A, Domain 1 / SAP domain superfamily / SAP domain / SAP motif profile. / Putative DNA-binding (bihelical) motif predicted to be involved in chromosomal organisation / SAP domain / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesSACCHAROMYCES CEREVISIAE (brewer's yeast)
MethodSOLUTION NMR / MANUAL ASSIGNMENT THEN SIMULATED ANNEALING
AuthorsDodson, C.A. / Ferguson, N. / Rutherford, T.J. / Johnson, C.M. / Fersht, A.R.
CitationJournal: Protein Eng.Des.Sel. / Year: 2010
Title: Engineering a Two-Helix Bundle Protein for Folding Studies.
Authors: Dodson, C.A. / Ferguson, N. / Rutherford, T.J. / Johnson, C.M. / Fersht, A.R.
History
DepositionAug 21, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 16, 2010Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 24, 2018Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name ..._entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain / _entity_src_gen.pdbx_host_org_variant
Revision 1.4May 15, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 / _pdbx_database_status.status_code_mr / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROTEIN THO1


Theoretical massNumber of molelcules
Total (without water)5,6551
Polymers5,6551
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)25 / 25STRUCTURES REACHING ACCEPTANCE CRITERIA OF MINIMUM RESTRAINT VIOLATION
Representative

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Components

#1: Protein PROTEIN THO1 / THO1


Mass: 5655.264 Da / Num. of mol.: 1 / Fragment: SAP DOMAIN, RESIDUES 2-50 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Plasmid: PRSETA DERIVATIVE / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / Variant (production host): C41 / References: UniProt: P40040
Compound detailsENGINEERED RESIDUE IN CHAIN A, LEU 30 TO TRP
Sequence detailsSEQUENCE NUMBERING FOR CONSTRUCT AS GIVEN, NOT FOR FULL- LENGTH PROTEIN. L31W MUTANT STRUCTURE SOLVED HERE.

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111NOESY
121COSY
131TOCSY
141HSQC
NMR detailsText: STRUCTURE DETERMINED USING TRIPLE-RESONANCE NMR SPECTROSCOPY ON 13C, 15N-LABELLED SAMPLE. STEREO-SPECIFIC ASSIGNMENT OF LEU AND VAL FROM 10PC-13C LABELLED SAMPLE.

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Sample preparation

DetailsContents: 95% WATER / 5% D20
Sample conditionsIonic strength: 500 mM / pH: 6 / Pressure: 1.0 atm / Temperature: 283.0 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CNS1.1BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU,READ, RICE,SIMONSON,WARRENrefinement
Sparkystructure solution
RefinementMethod: MANUAL ASSIGNMENT THEN SIMULATED ANNEALING / Software ordinal: 1
NMR ensembleConformer selection criteria: STRUCTURES REACHING ACCEPTANCE CRITERIA OF MINIMUM RESTRAINT VIOLATION
Conformers calculated total number: 25 / Conformers submitted total number: 25

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