[English] 日本語
Yorodumi- PDB-1adn: SOLUTION STRUCTURE OF THE DNA METHYLPHOSPHOTRIESTER REPAIR DOMAIN... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1adn | ||||||
---|---|---|---|---|---|---|---|
Title | SOLUTION STRUCTURE OF THE DNA METHYLPHOSPHOTRIESTER REPAIR DOMAIN OF ESCHERICHIA COLI ADA | ||||||
Components | N-ADA 10 | ||||||
Keywords | TRANSCRIPTION REGULATION | ||||||
Function / homology | Function and homology information : / methylated-DNA-[protein]-cysteine S-methyltransferase / methylated-DNA-[protein]-cysteine S-methyltransferase activity / : / DNA alkylation repair / sequence-specific DNA binding / methylation / 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 / sequence-specific DNA binding / methylation / 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 | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | SOLUTION NMR | ||||||
Authors | Myers, 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1adn.cif.gz | 227.5 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1adn.ent.gz | 173.2 KB | Display | PDB format |
PDBx/mmJSON format | 1adn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1adn_validation.pdf.gz | 352.5 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1adn_full_validation.pdf.gz | 488.2 KB | Display | |
Data in XML | 1adn_validation.xml.gz | 48.2 KB | Display | |
Data in CIF | 1adn_validation.cif.gz | 63.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ad/1adn ftp://data.pdbj.org/pub/pdb/validation_reports/ad/1adn | HTTPS FTP |
-Related structure data
Similar structure data |
---|
-Links
-Assembly
Deposited unit |
| |||||||||
---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||
NMR ensembles |
|
-Components
#1: Protein | 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 / |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR |
---|
-Sample preparation
Crystal grow | *PLUS Method: other / Details: NMR |
---|
-Processing
NMR software | Name: DGII / Developer: HAVEL / Classification: refinement |
---|---|
Refinement | Software 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 ensemble | Conformers submitted total number: 14 |