[English] 日本語
Yorodumi
- PDB-1adn: SOLUTION STRUCTURE OF THE DNA METHYLPHOSPHOTRIESTER REPAIR DOMAIN... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1adn
TitleSOLUTION STRUCTURE OF THE DNA METHYLPHOSPHOTRIESTER REPAIR DOMAIN OF ESCHERICHIA COLI ADA
ComponentsN-ADA 10
KeywordsTRANSCRIPTION REGULATION
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
AuthorsMyers, L.C. / Verdine, G.L. / Wagner, G.
Citation
Journal: Biochemistry / Year: 1993
Title: Solution structure of the DNA methyl phosphotriester repair domain of Escherichia coli Ada.
Authors: Myers, L.C. / Verdine, G.L. / Wagner, G.
#1: Journal: Science / Year: 1993
Title: Repair of DNA Methylphosphotriesters Through a Metalloactivated Cysteine Nucleophile
Authors: Myers, L.C. / Terranova, M.P. / Ferentz, A.E. / Wagner, G. / Verdine, G.L.
History
DepositionSep 30, 1993Processing site: BNL
Revision 1.0Jan 31, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 16, 2022Group: 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_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.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_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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: N-ADA 10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,5352
Polymers10,4701
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)14 / -
Representative

-
Components

#1: Protein N-ADA 10


Mass: 10469.978 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) 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

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR

-
Sample preparation

Crystal grow
*PLUS
Method: other / Details: NMR

-
Processing

NMR softwareName: DGII / Developer: HAVEL / Classification: refinement
RefinementSoftware ordinal: 1
Details: DATA WERE COLLECTED AT PH 6.4 AND AT 25 DEGREES CELSIUS. RESTRAINTS USED FOR THE STRUCTURE CALCULATIONS INCLUDED 547 NOE RESTRAINTS CONSISTING OF 108 INTRA-RESIDUE, 175 SEQUENTIAL, 91 MEDIUM (1<|I-J|<6) AND 173 LONG RANGE NOES. ADDITIONALLY, 50 HYDROGEN BONDING DISTANCES AS WELL AS DIHEDRAL ANGLE RESTRAINTS FOR 69 PHI ANGLES AND 8 CHI-1 ANGLES WERE INCLUDED. STEREOSPECIFIC ASSIGNMENTS HAVE BEEN MADE FOR THE METHYLENE PROTONS OF ASN 22, CYS 42, ASN 51, SER 53, PHE 54 AND TYR 55. STEREOSPECIFIC ASSIGNMENTS HAVE ALSO BEEN MADE FOR THE METHYL GROUPS OF VAL 16, LEU 17, VAL 28, LEU 48, VAL 52, LEU 62, AND LEU 84. THIS STUDY AND REFERENCE 1 ABOVE SHOW THAT CYS 38, CYS 42, CYS 69, AND CYS 72 ARE THE LIGANDS FOR A TIGHTLY BOUND ZINC ION. A 2.3 ANGSTROM THIOL - ZINC DISTANCE RESTRAINT WAS IMPOSED ON THE FOUR CYSTEINE METAL LIGANDS. ADDITIONAL DISTANCE AND DIHEDRAL RESTRAINTS WERE APPLIED TO ENFORCE A TETRAHEDRAL METAL LIGATION AND TO MAINTAIN PROPER SP3 HYBRIDIZATION GEOMETRIES OF THE COORDINATED SULFUR ATOMS. A DIHEDRAL ANGLE RESTRAINT MAINTAINS AN S TYPE LIGAND CONFIGURATION.
NMR ensembleConformers submitted total number: 14

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more