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- PDB-1l3g: NMR Structure of the DNA-binding Domain of Cell Cycle Protein, Mb... -

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Basic information

Entry
Database: PDB / ID: 1l3g
TitleNMR Structure of the DNA-binding Domain of Cell Cycle Protein, Mbp1(2-124) from Saccharomyces cerevisiae
ComponentsTRANSCRIPTION FACTOR Mbp1
KeywordsCELL CYCLE / Mlu 1 cell cycle box Binding Protein / winged helix-turn-helix proteins
Function / homology
Function and homology information


SBF transcription complex / MBF transcription complex / G1/S transition of mitotic cell cycle / DNA-binding transcription activator activity, RNA polymerase II-specific / sequence-specific DNA binding / regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / nucleus
Similarity search - Function
Transcription regulator HTH, APSES-type DNA-binding domain / KilA-N domain / Transcription regulator HTH, APSES-type DNA-binding domain / KilA, N-terminal/APSES-type HTH, DNA-binding / HTH APSES-type DNA-binding domain superfamily / APSES-type HTH DNA-binding domain profile. / KilA-N / Mlu1-box Binding Protein; DNA-binding Domain / Ankyrin repeats (many copies) / Ankyrin repeat ...Transcription regulator HTH, APSES-type DNA-binding domain / KilA-N domain / Transcription regulator HTH, APSES-type DNA-binding domain / KilA, N-terminal/APSES-type HTH, DNA-binding / HTH APSES-type DNA-binding domain superfamily / APSES-type HTH DNA-binding domain profile. / KilA-N / Mlu1-box Binding Protein; DNA-binding Domain / Ankyrin repeats (many copies) / Ankyrin repeat / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
Transcription factor MBP1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodSOLUTION NMR / simulated annealing, energy minimization
AuthorsNair, M. / McIntosh, P.B. / Frenkiel, T.A. / Kelly, G. / Taylor, I.A. / Smerdon, S.J. / Lane, A.N.
CitationJournal: Biochemistry / Year: 2003
Title: NMR Structure of the DNA-Binding Domain of the Cell Cycle Protein Mbp1 from Saccharomyces cerevisiae
Authors: Nair, M. / McIntosh, P.B. / Frenkiel, T.A. / Kelly, G. / Taylor, I.A. / Smerdon, S.J. / Lane, A.N.
History
DepositionFeb 27, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 18, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 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 / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TRANSCRIPTION FACTOR Mbp1


Theoretical massNumber of molelcules
Total (without water)15,4681
Polymers15,4681
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)19 / 1000A total of 1000 conformers calculated. 100 conformers with low target function selected for refinement. Final set comprises 19 conformers with least restraint violation.
RepresentativeModel #9closest to the average

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Components

#1: Protein TRANSCRIPTION FACTOR Mbp1


Mass: 15467.536 Da / Num. of mol.: 1 / Fragment: DNA-BINDING DOMAIN (RESIDUES 2-124)
Source method: isolated from a genetically manipulated source
Details: MLU 1 CELL CYCLE BOX BINDING PROTEIN
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21/DE3 / References: UniProt: P39678

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
2223D 13C-separated NOESY
333HNHA
NMR detailsText: 2D J-modulated HSQC experiments were recorded on partially aligned U15N labelled sample to measure residual dipolar couplings

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Sample preparation

Details
Solution-IDContentsSolvent system
1Mbp1 U-15N,13C 40mM Na-Phosphate, 100mM NaCl90% H2O/10% D2O
2Mbp1 U-15N, 40mM Na-Phosphate, 100mM NaCl90% H2O/10% D2O
Sample conditionspH: 7.6 / Temperature: 288 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA6001
Varian UNITYVarianUNITY6002
Varian UNITYPLUSVarianUNITYPLUS5003

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Processing

NMR software
NameVersionDeveloperClassification
DYANA1.5Guntertstructure solution
NMRPipe1.8Delaglioprocessing
VNMR6.1BVariancollection
X-PLOR3.8Brungerrefinement
TALOS98.040.21.02Cornilescustructure solution
RefinementMethod: simulated annealing, energy minimization / Software ordinal: 1
Details: 13 C-terminal tag residues (KLAAALEHHHHHH) were excluded from structure calculations.
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: A total of 1000 conformers calculated. 100 conformers with low target function selected for refinement. Final set comprises 19 conformers with least restraint violation.
Conformers calculated total number: 1000 / Conformers submitted total number: 19

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