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- PDB-2adr: ADR1 DNA-BINDING DOMAIN FROM SACCHAROMYCES CEREVISIAE, NMR, 25 ST... -

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Basic information

Entry
Database: PDB / ID: 2adr
TitleADR1 DNA-BINDING DOMAIN FROM SACCHAROMYCES CEREVISIAE, NMR, 25 STRUCTURES
ComponentsADR1
KeywordsTRANSCRIPTION REGULATION / ADR1 / ZINC FINGER
Function / homology
Function and homology information


positive regulation of peroxisome organization / positive regulation of ethanol catabolic process / peroxisome organization / positive regulation of fatty acid beta-oxidation / TFIID-class transcription factor complex binding / TFIIB-class transcription factor binding / cellular response to ethanol / chromatin organization / molecular adaptor activity / sequence-specific DNA binding ...positive regulation of peroxisome organization / positive regulation of ethanol catabolic process / peroxisome organization / positive regulation of fatty acid beta-oxidation / TFIID-class transcription factor complex binding / TFIIB-class transcription factor binding / cellular response to ethanol / chromatin organization / molecular adaptor activity / sequence-specific DNA binding / nucleic acid binding / RNA polymerase II-specific DNA-binding transcription factor binding / DNA-binding transcription factor activity, RNA polymerase II-specific / transcription coactivator activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / regulation of transcription by RNA polymerase II / chromatin / positive regulation of transcription by RNA polymerase II / zinc ion binding / nucleus / cytoplasm / cytosol
Similarity search - Function
: / Classic Zinc Finger / Zinc finger, C2H2 type / Double Stranded RNA Binding Domain / zinc finger / Zinc finger C2H2 type domain profile. / Zinc finger C2H2 superfamily / Zinc finger C2H2 type domain signature. / Zinc finger C2H2-type / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Regulatory protein ADR1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodSOLUTION NMR / DISTANCE GEOMETRY, SIMULATED ANNEALING
AuthorsBowers, P.M. / Kleivt, R.E.
Citation
Journal: Nat.Struct.Biol. / Year: 1999
Title: A folding transition and novel zinc finger accessory domain in the transcription factor ADR1.
Authors: Bowers, P.M. / Schaufler, L.E. / Klevit, R.E.
#1: Journal: To be Published
Title: A Disorder-to-Order Transition Couled to DNA Binding in the Essential Zinc-Finger DNA-Binding of Yeast Adr1 Elucidated by Backbone Dynamics and Proton Exchange
Authors: Hyre, D.E. / Klevit, R.E.
#2: Journal: Protein Sci. / Year: 1997
Title: NMR Chemical Shift Perturbation Mapping of DNA Binding by a Zinc-Finger Domain from the Yeast Transcription Factor Adr1
Authors: Schmiedeskamp, M. / Rajagopal, P. / Klevit, R.E.
History
DepositionMar 20, 1998Processing site: BNL
Revision 1.0Jun 17, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_conn_angle / pdbx_struct_oper_list / 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.process_site / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_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 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ADR1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,2573
Polymers7,1261
Non-polymers1312
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)25 / 50LOWEST ENERGY TERM
Representative

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Components

#1: Protein ADR1


Mass: 7126.188 Da / Num. of mol.: 1 / Fragment: DNA-BINDING DOMAIN / Mutation: C140A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Cell line: BL21 / Plasmid: PET11A / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P07248
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
11113C EDITED NOESY
12115N EDITED NOESY
131HNHB

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Sample preparation

Sample conditionspH: 5.5 / Temperature: 303 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: Bruker DMX750 / Manufacturer: Bruker / Model: DMX750 / Field strength: 750 MHz

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
X-PLOR3.1phasing
NMR software
NameVersionDeveloperClassification
X-PLOR3.1BRUNGERrefinement
NMRPIPESstructure solution
X-PLORstructure solution
RefinementMethod: DISTANCE GEOMETRY, SIMULATED ANNEALING / Software ordinal: 1
Details: REFINEMENT DETAILS HAVE BEEN SUBMITTED FOR PUBLICATION.
NMR ensembleConformer selection criteria: LOWEST ENERGY TERM / Conformers calculated total number: 50 / Conformers submitted total number: 25

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