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- PDB-1eyf: REFINED STRUCTURE OF THE DNA METHYL PHOSPHOTRIESTER REPAIR DOMAIN... -

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Basic information

Entry
Database: PDB / ID: 1eyf
TitleREFINED STRUCTURE OF THE DNA METHYL PHOSPHOTRIESTER REPAIR DOMAIN OF E. COLI ADA
ComponentsADA REGULATORY PROTEIN
KeywordsDNA BINDING PROTEIN / One central beta-sheet sandwiched between two alpha-helices
Function / homology
Function and homology information


: / methylated-DNA-[protein]-cysteine S-methyltransferase / methylated-DNA-[protein]-cysteine S-methyltransferase activity / DNA alkylation repair / : / methylation / sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / DNA damage response ...: / methylated-DNA-[protein]-cysteine S-methyltransferase / methylated-DNA-[protein]-cysteine S-methyltransferase activity / DNA alkylation repair / : / methylation / sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / DNA damage response / positive regulation of DNA-templated transcription / zinc ion binding
Similarity search - Function
DNA Methylphosphotriester Repair Domain / DNA Methylphosphotriester Repair Domain / Ada DNA repair, metal-binding / Bifunctional regulatory protein Ada / Ada-like domain superfamily / Metal binding domain of Ada / Methylguanine DNA methyltransferase, ribonuclease-like domain / 6-O-methylguanine DNA methyltransferase, ribonuclease-like domain / Methylated DNA-protein cysteine methyltransferase domain superfamily / Methylated-DNA-[protein]-cysteine S-methyltransferase, active site ...DNA Methylphosphotriester Repair Domain / DNA Methylphosphotriester Repair Domain / Ada DNA repair, metal-binding / Bifunctional regulatory protein Ada / Ada-like domain superfamily / Metal binding domain of Ada / Methylguanine DNA methyltransferase, ribonuclease-like domain / 6-O-methylguanine DNA methyltransferase, ribonuclease-like domain / Methylated DNA-protein cysteine methyltransferase domain superfamily / Methylated-DNA-[protein]-cysteine S-methyltransferase, active site / Methylated-DNA--protein-cysteine methyltransferase active site. / HTH domain AraC-type, conserved site / Bacterial regulatory proteins, araC family signature. / Methylated-DNA-[protein]-cysteine S-methyltransferase, DNA binding / Methylated DNA-protein cysteine methyltransferase, DNA binding domain / 6-O-methylguanine DNA methyltransferase, DNA binding domain / DNA binding HTH domain, AraC-type / Helix-turn-helix domain / Bacterial regulatory proteins, araC family DNA-binding domain profile. / helix_turn_helix, arabinose operon control protein / Homeobox-like domain superfamily / Winged helix-like DNA-binding domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Bifunctional transcriptional activator/DNA repair enzyme Ada
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodSOLUTION NMR / distance geometry
AuthorsLin, Y. / Dotsch, V. / Wintner, T. / Peariso, K. / Myers, L.C. / Penner-Hahn, J.E. / Verdine, G.L. / Wagner, G.
CitationJournal: Biochemistry / Year: 2001
Title: Structural basis for the functional switch of the E. coli Ada protein
Authors: Lin, Y. / Dotsch, V. / Wintner, T. / Peariso, K. / Myers, L.C. / Penner-Hahn, J.E. / Verdine, G.L. / Wagner, G.
History
DepositionMay 6, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 9, 2003Provider: 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_oper_list / struct_conn / 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 / _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_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: ADA REGULATORY PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,5352
Polymers10,4701
Non-polymers651
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)25 / 50structures with the lowest energy
RepresentativeModel #13lowest energy

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Components

#1: Protein ADA REGULATORY PROTEIN


Mass: 10469.978 Da / Num. of mol.: 1 / Fragment: N-TERMINAL 10 KDA DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: PADA39 / Production host: Escherichia coli (E. coli) / References: UniProt: P06134
#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
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
2222D NOESY
3333D 15N-separated NOESY
343HNHA
NMR detailsText: This structure was determined using standard 2D homonuclear and 3D heteronuclear techinques

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Sample preparation

Details
Solution-IDContentsSolvent system
12 mM N-Ada10; 25 mM sodium phosphate buffer pH 6.4, 50 mM NaCl, and 10 mM 2-mercaptoethanol; 90% H2O, 10% D2O90% H2O/10% D2O
22 mM N-Ada10; 25 mM sodium phosphate buffer pH 6.4, 50 mM NaCl, and 10 mM 2-mercaptoethanol; 100% D2O90% H2O/10% D2O
32 mM N-Ada10 U-15N; 25 mM sodium phosphate buffer pH 6.4, 50 mM NaCl, and 10 mM 2-mercaptoethanol; 90% H2O, 10% D2O100% D2O
42 mM N-Ada10 U-15N, 13C; 25 mM sodium phosphate buffer pH 6.4, 50 mM NaCl, and 10 mM 2-mercaptoethanol; 90% H2O, 10% D2O90% H2O/10% D2O
Sample conditions
Conditions-IDpHPressure (kPa)Temperature (K)
16.4 ambient 298 K
26.4 ambient 298 K
36.4 ambient 298 K
46.4 ambient 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AMXBrukerAMX5001
Bruker AMXBrukerAMX6002
Varian VXRSVarianVXRS5003
Varian UNITYVarianUNITY5004
Varian UNITYPLUSVarianUNITYPLUS4005
Varian UNITYPLUSVarianUNITYPLUS7506

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Processing

NMR software
NameVersionDeveloperClassification
UXNMRcollection
VNMRcollection
Felix95processing
XEASYBrartels et aldata analysis
DGIIHavel et alstructure solution
DGIIHavel et alrefinement
RefinementMethod: distance geometry / Software ordinal: 1
Details: the structures are based on a total of 1014 restraints, 872 are NOE-derived distance constraints, 82 dihedral angle restraints,46 distance restraints from hydrogen bonds, and 14 zinc cluster distance restraints
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 25

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