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- PDB-1f4s: STRUCTURE OF TRANSCRIPTIONAL FACTOR ALCR IN COMPLEX WITH A TARGET DNA -

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Basic information

Entry
Database: PDB / ID: 1f4s
TitleSTRUCTURE OF TRANSCRIPTIONAL FACTOR ALCR IN COMPLEX WITH A TARGET DNA
Components
  • DNA (5'-D(P*CP*GP*TP*GP*CP*GP*GP*AP*TP*C)-3')
  • DNA (5'-D(P*GP*AP*TP*CP*CP*GP*CP*AP*CP*G)-3')
  • ETHANOL REGULON TRANSCRIPTIONAL FACTOR
KeywordsTRANSCRIPTION/DNA / PROTEIN-DNA COMPLEX / ZINC BINUCLEAR CLUSTER PROTEIN / TRANSCRIPTION-DNA COMPLEX
Function / homology
Function and homology information


acetaldehyde catabolic process / L-threonine catabolic process / ethanol catabolic process / DNA-binding transcription factor activity, RNA polymerase II-specific / chromatin remodeling / DNA-binding transcription factor activity / positive regulation of transcription by RNA polymerase II / DNA binding / zinc ion binding / nucleus
Similarity search - Function
: / Zn(2)-C6 fungal-type DNA-binding domain / CD2-Gal4 / Fungal Zn(2)-Cys(6) binuclear cluster domain / Zn(2)-C6 fungal-type DNA-binding domain superfamily / Zn(2)-C6 fungal-type DNA-binding domain profile. / GAL4-like Zn(II)2Cys6 (or C6 zinc) binuclear cluster DNA-binding domain / Zn(2)-C6 fungal-type DNA-binding domain / Few Secondary Structures / Irregular
Similarity search - Domain/homology
DNA / Regulatory protein alcR
Similarity search - Component
Biological speciesEmericella nidulans (mold)
MethodSOLUTION NMR / distance geometry, simulated annealing
AuthorsCahuzac, B. / Cerdan, R. / Felenbok, B. / Guittet, E.
CitationJournal: Structure / Year: 2001
Title: The solution structure of an AlcR-DNA complex sheds light onto the unique tight and monomeric DNA binding of a Zn(2)Cys(6) protein.
Authors: Cahuzac, B. / Cerdan, R. / Felenbok, B. / Guittet, E.
History
DepositionJun 9, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 28, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / 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_nmr_software.name / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_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: DNA (5'-D(P*CP*GP*TP*GP*CP*GP*GP*AP*TP*C)-3')
B: DNA (5'-D(P*GP*AP*TP*CP*CP*GP*CP*AP*CP*G)-3')
P: ETHANOL REGULON TRANSCRIPTIONAL FACTOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,8025
Polymers13,6713
Non-polymers1312
Water181
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 20The submitted conformer models are the 10 structures with the lowest energy.
Representative

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Components

#1: DNA chain DNA (5'-D(P*CP*GP*TP*GP*CP*GP*GP*AP*TP*C)-3')


Mass: 3061.003 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: ALCR CONSENSUS HALF-TARGET
#2: DNA chain DNA (5'-D(P*GP*AP*TP*CP*CP*GP*CP*AP*CP*G)-3')


Mass: 3029.993 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: ALCR CONSENSUS HALF-TARGET
#3: Protein ETHANOL REGULON TRANSCRIPTIONAL FACTOR / REGULATORY PROTEIN ALCR


Mass: 7580.351 Da / Num. of mol.: 1 / Mutation: N-TERMINAL DNA-BINDING DOMAIN, RESIDUES 1-60
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Emericella nidulans (mold) / Production host: Escherichia coli (E. coli) / References: UniProt: P21228
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1213D 15N-separated NOESY
131HNHA

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Sample preparation

DetailsContents: 1 mM AlcR U-15N, 1.1 mM double stranded DNA
Solvent system: 20 mM phosphate buffer; 90%H2O, 10%D2O; pH 5.9
Sample conditionspH: 5.9 / Pressure: 1 atm / Temperature: 293 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
Bruker DRXBrukerDRX8001
Bruker DMXBrukerDMX6002

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2.1processing
Gifa4Delsuc, M.A.processing
DIANAGntertstructure solution
X-PLOR3.1Brungerrefinement
RefinementMethod: distance geometry, simulated annealing / Software ordinal: 1
Details: 1142 noe-derived constraints, 76 h-bond constraints, 33 phi angle restraints, 118 loose angle restraints on the DNA backbone
NMR ensembleConformer selection criteria: The submitted conformer models are the 10 structures with the lowest energy.
Conformers calculated total number: 20 / Conformers submitted total number: 10

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