1DIZ Hydrolase Dna date Nov 30, 1999
title Crystal Structure Of E. Coli 3-Methyladenine Dna Glycosylase Complexed With Dna
authors T.Hollis, Y.Ichikawa, T.E.Ellenberger
compound source
Molecule: Dna (5'-D(Gpapcpaptpgpap(Nri)Ptpgpcpc
Chain: C, E
Engineered: Yes
Synthetic: Yes
Organism_scientific: Escherichia Coli
Organism_taxid: 562
Other_details: This Sequence Occurs Naturally In E. Coli

Molecule: Dna (5'-D(Gpgpcpapaptpcpaptpgptpcpa)
Chain: D, F
Engineered: Yes

Synthetic: Yes
Organism_scientific: Escherichia Coli
Organism_taxid: 562
Other_details: This Sequence Occurs Naturally In E. Coli

Molecule: 3-Methyladenine Dna Glycosylase II
Chain: A, B
Synonym: 3-Methyladenine-Dna Glycosylase II, Inducible, Tag
Ec: 3.2.2.21
Engineered: Yes

Organism_scientific: Escherichia Coli
Organism_taxid: 562
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: P 31 2 1
R_factor 0.250 R_Free 0.290
crystal
cell
length a length b length c angle alpha angle beta angle gamma
82.400 82.400 199.700 90.00 90.00 120.00
method X-Ray Diffractionresolution 2.50 Å
ligand NA, NRI enzyme Hydrolase E.C.3.2.2.21 BRENDA
related structures by homologous chain: 1PVS
Gene
Ontology
ChainFunctionProcessComponent
A, B


Primary referenceDNA bending and a flip-out mechanism for base excision by the helix-hairpin-helix DNA glycosylase, Escherichia coli AlkA., Hollis T, Ichikawa Y, Ellenberger T, EMBO J 2000 Feb 15;19(4):758-66. PMID:10675345
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (119 Kb) [Save to disk]
  • Biological Unit Coordinates (1diz.pdb1.gz) 58 Kb
  • Biological Unit Coordinates (1diz.pdb2.gz) 58 Kb
  • LPC: Ligand-Protein Contacts for 1DIZ
  • CSU: Contacts of Structural Units for 1DIZ
  • Likely Quarternary Molecular Structure file(s) for 1DIZ
  • Retrieve 1DIZ in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1DIZ from S2C, [Save to disk]
  • View 1DIZ in 3D
  • Proteopedia, because life has more than 2D.
  • On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.
  • On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.
  • Visual 3D analysis of 1DIZ
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 1DIZ, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1diza2, region A:1-99 [Jmol] [rasmolscript] [script source]
        - Domain d1diza1, region A:100-282 [Jmol] [rasmolscript] [script source]
        - Domain d1dizb2, region B:1-99 [Jmol] [rasmolscript] [script source]
        - Domain d1dizb1, region B:100-282 [Jmol] [rasmolscript] [script source]
  • Fold representative 1diz from FSSP and Dali (Families of Structurally Similar Proteins)
  • Class (fold), Architecture (subfold), Topology, Homologous superfamily from CATH
  • Summaries and structural analyses of PDB data files from PDBSum
  • Identification of Protein Pockets & Cavities at CASTp
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1diz] [1diz_D] [1diz_C] [1diz_E] [1diz_F] [1diz_A] [1diz_B]
  • SWISS-PROT database: [P04395]
  • Domain organization of [3MG2_ECOLI] by SWISSPFAM
  • Domains found in 1DIZ: [AlkA_N] [ENDO3c ] by SMART
  • Other resources with information on 1DIZ
  • Community annotation for 1DIZ at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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