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- PDB-1wpk: Methylated Form of N-terminal Transcriptional Regulator Domain of... -

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Basic information

Entry
Database: PDB / ID: 1wpk
TitleMethylated Form of N-terminal Transcriptional Regulator Domain of Escherichia Coli Ada Protein
ComponentsADA regulatory protein
KeywordsDNA BINDING PROTEIN / ZINC COORDINATION / HELIX-TURN-HELIX
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 / Bacterial regulatory helix-turn-helix proteins, AraC family / Methylguanine DNA methyltransferase, ribonuclease-like domain / 6-O-methylguanine DNA methyltransferase, ribonuclease-like domain / Methylated DNA-protein cysteine methyltransferase domain superfamily ...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 / Bacterial regulatory helix-turn-helix proteins, AraC family / 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 / Homeodomain-like / Homeobox-like domain superfamily / Arc Repressor Mutant, subunit A / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / 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, simulated annealing, torsion angle dynamics
AuthorsTakinowaki, H. / Matsuda, Y. / Yoshida, T. / Kobayashi, Y. / Ohkubo, T.
CitationJournal: Protein Sci. / Year: 2006
Title: The solution structure of the methylated form of the N-terminal 16-kDa domain of Escherichia coli Ada protein
Authors: Takinowaki, H. / Matsuda, Y. / Yoshida, T. / Kobayashi, Y. / Ohkubo, T.
History
DepositionSep 7, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 13, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_oper_list / struct_conn / struct_conn_type / 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 / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_conn_type.id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ADA regulatory protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,7322
Polymers16,6661
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)17 / 25The submitted conformer models are the 17 structures with the lowest energy
RepresentativeModel #12lowest energy

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Components

#1: Protein ADA regulatory protein / Regulatory protein of adaptative response


Mass: 16666.172 Da / Num. of mol.: 1 / Fragment: Methylated N-terminal 16 kDa Domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: ada / Plasmid: pET22b / Species (production host): Escherichia coli / Production host: Escherichia coli K12 (bacteria) / Strain (production host): K12 / 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
1113D 15N-separated NOESY
1223D 13C-separated NOESY
NMR detailsText: The structure was determined using triple-resonance NMR spectroscopy.

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Sample preparation

Details
Solution-IDContentsSolvent system
11mM Protein U-15N,13C; 50mM phosphate buffer with 5mM 2-mercaptoethanol NA; 85% H2O, 15% D2O85% H2O, 15% D2O
21mM Protein U-15N,13C; 50mM phosphate buffer with 5mM 2-mercaptoethanol ; 99.9% D2O99.9% D2O
Sample conditionsIonic strength: 300mM NaCl / pH: 6.5 / Pressure: ambient / Temperature: 303 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

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Processing

NMR software
NameVersionClassification
CNS1.1structure solution
CNS1.1refinement
RefinementMethod: distance geometry, simulated annealing, torsion angle dynamics
Software ordinal: 1
Details: The structures are based on a total of 1991 restraints; 1735 are NOE-derived distance constraints, 148 dihedral angle restraints, 94 distance restraints from hydrogen bonds and 14 zinc- ...Details: The structures are based on a total of 1991 restraints; 1735 are NOE-derived distance constraints, 148 dihedral angle restraints, 94 distance restraints from hydrogen bonds and 14 zinc-thiolate center distance restraints.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: The submitted conformer models are the 17 structures with the lowest energy
Conformers calculated total number: 25 / Conformers submitted total number: 17

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