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- PDB-2lo2: Solution structure of Sgf11(63-99) zinc finger domain -

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Basic information

Entry
Database: PDB / ID: 2lo2
TitleSolution structure of Sgf11(63-99) zinc finger domain
ComponentsSAGA-associated factor 11
KeywordsTRANSCRIPTION / ZINC-FINGER / DEUBIQUITINATION / TRANSCRIPTION FACTOR / SAGA COMPLEX
Function / homology
Function and homology information


DUBm complex / SLIK (SAGA-like) complex / SAGA complex / enzyme activator activity / chromatin organization / transcription coactivator activity / regulation of transcription by RNA polymerase II / zinc ion binding / nucleus
Similarity search - Function
Yeast SAGA-associated factor 11, N-terminal domain / SAGA-associated factor 11 N-terminal domain / SAGA complex, Sgf11 subunit / Sgf11 (transcriptional regulation protein)
Similarity search - Domain/homology
SAGA-associated factor 11
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodSOLUTION NMR / torsion angle dynamics
Model detailslowest energy, model 4
AuthorsGao, X. / Koehler, C. / Bonnet, J. / Devys, D. / Kieffer, B.
CitationJournal: To be Published
Title: Insights into the role of SGF11 and SGF73 for the interaction between SAGA and nucleosomes
Authors: Koehler, C. / Gao, X. / Bonnet, J. / Devys, D. / Kieffer, B.
History
DepositionJan 10, 2012Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jan 25, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2May 15, 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: SAGA-associated factor 11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,3742
Polymers4,3091
Non-polymers651
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide SAGA-associated factor 11 / 11 kDa SAGA-associated factor


Mass: 4308.829 Da / Num. of mol.: 1 / Fragment: SGF11-type zinc finger residues 63-99
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: SGF11, YPL047W / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q03067
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
Details: CCHC zinc finger domain of SAGA-associated factor 11
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC aliphatic
1312D 1H-1H TOCSY
1412D 1H-1H COSY
1512D 1H-1H NOESY
1613D CBCA(CO)NH
1713D HNCO
1813D HNCA
1913D HN(CA)CB
11013D HN(CO)CA
11113D (H)CCH-TOCSY
11213D 1H-15N NOESY
11313D 1H-13C NOESY aliphatic
11413D HN(CA)CO
11512D 1H-15N HSQC R1 edited
11612D 1H-15N HSQC R2 edited
11712D 1H-15N heteronuclear NOE

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Sample preparation

DetailsContents: 0.7 mM [U-99% 13C; U-98% 15N] sgf11, 20 mM sodium phosphate, 75 mM sodium chloride, 1 mM DTT, 10 % D2O, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.7 mMsgf11-1[U-99% 13C; U-98% 15N]1
20 mMsodium phosphate-21
75 mMsodium chloride-31
1 mMDTT-41
10 %D2O-51
Sample conditionsIonic strength: 0.115 / pH: 7.0 / Pressure: ambient / Temperature: 285 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE7001
Bruker AvanceBrukerAVANCE6002

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Processing

NMR software
NameDeveloperClassification
TopSpinBruker Biospincollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRViewJohnson, One Moon Scientificpeak picking
NMRViewJohnson, One Moon Scientificchemical shift assignment
NMRViewJohnson, One Moon Scientificdata analysis
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
TALOSCornilescu, Delaglio and Baxgeometry optimization
SparkyGoddarddata analysis
RefinementMethod: torsion angle dynamics / Software ordinal: 1 / Details: RECOORD scripts
NMR constraintsNOE constraints total: 1073 / NOE intraresidue total count: 435 / NOE long range total count: 151 / NOE medium range total count: 185 / NOE sequential total count: 302 / Hydrogen bond constraints total count: 22 / Protein chi angle constraints total count: 0 / Protein other angle constraints total count: 0 / Protein phi angle constraints total count: 22 / Protein psi angle constraints total count: 22
NMR representativeSelection criteria: lowest energy
NMR ensembleAverage torsion angle constraint violation: 0.06 °
Conformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20 / Maximum torsion angle constraint violation: 2.7 ° / Maximum upper distance constraint violation: 0.256 Å
NMR ensemble rmsDistance rms dev: 0.015 Å / Distance rms dev error: 0.005 Å

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