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- PDB-2jvl: NMR structure of the C-terminal domain of MBF1 of Trichoderma reesei -

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Basic information

Entry
Database: PDB / ID: 2jvl
TitleNMR structure of the C-terminal domain of MBF1 of Trichoderma reesei
ComponentsTrMBF1
KeywordsTRANSCRIPTION / MBF1 / Coactivator / Trichoderma reesei / helix-turn-helix / PROTEIN BINDING
Function / homology
Function and homology information


Helix-turn-helix / Helix-turn-helix XRE-family like proteins / Cro/C1-type HTH domain profile. / lambda repressor-like DNA-binding domains / Cro/C1-type helix-turn-helix domain / 434 Repressor (Amino-terminal Domain) / Lambda repressor-like, DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Multiprotein-bridging factor 1
Similarity search - Component
Biological speciesTrichoderma reesei (fungus)
MethodSOLUTION NMR / simulated annealing
Model detailsNMR structure of the C-terminal domain of MBF1 of Trichoderma reesei
AuthorsKopke Salinas, R. / Tomaselli, S. / Camilo, C.M. / Valencia, E.Y. / Farah, C.S. / El-Dorry, H. / Chambergo, F.S.
CitationJournal: Proteins / Year: 2009
Title: Solution structure of the C-terminal domain of multiprotein bridging factor 1 (MBF1) of Trichoderma reesei.
Authors: Salinas, R.K. / Camilo, C.M. / Tomaselli, S. / Valencia, E.Y. / Farah, C.S. / El-Dorry, H. / Chambergo, F.S.
History
DepositionSep 20, 2007Deposition site: BMRB / Processing site: RCSB
Revision 1.0Sep 2, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jan 31, 2018Group: Derived calculations / Structure summary
Category: audit_author / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _audit_author.name
Revision 1.3May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TrMBF1


Theoretical massNumber of molelcules
Total (without water)11,5281
Polymers11,5281
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein TrMBF1


Mass: 11528.153 Da / Num. of mol.: 1 / Fragment: C-terminal domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trichoderma reesei (fungus) / Plasmid details: pPROEX-HTa / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: D0VWW6*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
Details: NMR structure of the C-terminal domain of MBF1 of Trichoderma reesei
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 1H-13C NOESY
1213D 1H-15N NOESY
1312D 1H-1H NOESY
1423D 1H-13C NOESY
1522D 1H-1H NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
120 mM sodium phosphate, 100 mM sodium choloride, 5 % D2O, 95% H2O/5% D2O95% H2O/5% D2O
220 mM sodium phosphate, 100 mM sodium choloride, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentSolution-ID
20 mMsodium phosphate1
100 mMsodium choloride1
5 %D2O1
20 mMsodium phosphate2
100 mMsodium choloride2
Sample conditionsIonic strength: 0.151 / pH: 6.0 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA6001
Bruker DRXBrukerDRX5002

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Processing

NMR software
NameVersionDeveloperClassification
NMRView5.2.2Johnson, One Moon Scientificdata processing
CCPNMR1.0.14CCPNdata analysis
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
HADDOCK2Dominguez, Boelens, Bonvinrefinement
RefinementMethod: simulated annealing / Software ordinal: 1 / Details: water refinement with Haddock2.0 using CNS
NMR constraintsNOE constraints total: 1216 / NOE intraresidue total count: 378 / NOE long range total count: 255 / NOE medium range total count: 247 / NOE sequential total count: 336 / Protein phi angle constraints total count: 44 / Protein psi angle constraints total count: 44
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20 / Maximum upper distance constraint violation: 15 Å
NMR ensemble rmsDistance rms dev: 3.35 Å / Distance rms dev error: 1.15 Å

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