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- PDB-4d7x: Solution Structure of the Mediator Gall11 KIX Domain of C. Glabrata -

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Basic information

Entry
Database: PDB / ID: 4d7x
TitleSolution Structure of the Mediator Gall11 KIX Domain of C. Glabrata
ComponentsMEDIATOR OF RNA POLYMERASE II TRANSCRIPTION SUBUNIT 15
KeywordsTRANSCRIPTION
Function / homology
Function and homology information


mediator complex / transcription coregulator activity / regulation of transcription by RNA polymerase II
Similarity search - Function
Mediator complex, subunit Med15, fungi / Gal11, coactivator domain / Mediator complex subunit 15, KIX domain / Mediator complex subunit 15 / KIX domain / Gal11 activator-binding domain (ABD1) / Coactivator CBP, KIX domain / Coactivator CBP, KIX domain superfamily / Serum Albumin; Chain A, Domain 1 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Mediator of RNA polymerase II transcription subunit 15
Similarity search - Component
Biological speciesCANDIDA GLABRATA (fungus)
MethodSOLUTION NMR / CYANA, AMBER
AuthorsBoeszoermenyi, A. / Wagner, G. / Naar, A.M. / Arthanari, H.
CitationJournal: Nature / Year: 2016
Title: Inhibiting Fungal Multidrug Resistance by Disrupting an Activator-Mediator Interaction.
Authors: Nishikawa, J.L. / Boeszoermenyi, A. / Vale-Silva, L.A. / Torelli, R. / Posteraro, B. / Sohn, Y. / Ji, F. / Gelev, V. / Sanglard, D. / Sanguinetti, M. / Sadreyev, R.I. / Mukherjee, G. / ...Authors: Nishikawa, J.L. / Boeszoermenyi, A. / Vale-Silva, L.A. / Torelli, R. / Posteraro, B. / Sohn, Y. / Ji, F. / Gelev, V. / Sanglard, D. / Sanguinetti, M. / Sadreyev, R.I. / Mukherjee, G. / Bhyravabhotla, J. / Buhrlage, S.J. / Gray, N.S. / Wagner, G. / Naar, A.M. / Arthanari, H.
History
DepositionNov 30, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 9, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 17, 2016Group: Database references
Revision 1.2Mar 2, 2016Group: Database references
Revision 2.0Oct 23, 2019Group: Atomic model / Data collection / Other
Category: atom_site / pdbx_database_status ...atom_site / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _atom_site.Cartn_x / _atom_site.Cartn_y ..._atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _pdbx_database_status.status_code_cs / _pdbx_database_status.status_code_mr / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 2.1Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 2.2Jun 19, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: MEDIATOR OF RNA POLYMERASE II TRANSCRIPTION SUBUNIT 15


Theoretical massNumber of molelcules
Total (without water)9,7431
Polymers9,7431
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 10LOWEST ENERGY
RepresentativeModel #1

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Components

#1: Protein MEDIATOR OF RNA POLYMERASE II TRANSCRIPTION SUBUNIT 15 / MEDIATOR COMPLEX SUBUNIT 15 / TRANSCRIPTION REGULATORY PROTE IN GAL11 / C. GLABRATA GAL11A KIX DOMAIN


Mass: 9743.164 Da / Num. of mol.: 1 / Fragment: KIX DOMAIN, RESIDUES 1-86
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CANDIDA GLABRATA (fungus) / Plasmid: PET24B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q6FRS9

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111CG 15NHSQC
22115NNOESY
33113CHSQC ANOESY
44113CNOESY
551BRUKER ILV HSQC
NMR detailsText: BACKBONE AND SIDE-CHAIN RESONANCES WERE ASSIGNED USING TRIPLE-RESONANCE MNR SPECTROSCOPY. THE STRUCTURE WAS CALCULATED FROM NOES FROM 15N - AND 13C - FILTERED NOESY EXPERIMENTS.

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Sample preparation

Details
Solution-IDContents
193% H2O/7% D2O
293% H2O/7% D2O
393% H2O/7% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
11506.51.0 atm298.15 K
21506.51.0 atm298.15 K
31506.51.0 atm298.15 K
41506.51.0 atm298.15 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE6001
Varian INOVAVarianINOVA9002
7003
8004

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Processing

NMR software
NameVersionDeveloperClassification
AmberI. BERTINI, D.A. CASE, L. FERELLA, A. GIACHETTI, A. ROSATOrefinement
CcpNmr Analysis2.1structure solution
NMRPipeANYstructure solution
NMRDrawANYstructure solution
CcpNmr Analysis2.4structure solution
TALOS+2009.0605.17structure solution
CYANA3structure solution
RefinementMethod: CYANA, AMBER / Software ordinal: 1
Details: STRUCTURE REFINEMENT WAS PERFORMED THROUGH THE WENMR WEB-INTERACE WITH AMBER. BERTINI, I., CASE, D. A., FERELLA, L., GIACHETTI, A. & ROSATO, A., 2011, A GRID-ENABLED WEB PORTAL FOR NMR ...Details: STRUCTURE REFINEMENT WAS PERFORMED THROUGH THE WENMR WEB-INTERACE WITH AMBER. BERTINI, I., CASE, D. A., FERELLA, L., GIACHETTI, A. & ROSATO, A., 2011, A GRID-ENABLED WEB PORTAL FOR NMR STRUCTURE REFINEMENT WITH AMBER. BIOINFORMATICS 27, 2384- -2390
NMR ensembleConformer selection criteria: LOWEST ENERGY / Conformers calculated total number: 10 / Conformers submitted total number: 10

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