1RDD Hydrolase(Endoribonuclease) date Jun 23, 1993
title Crystal Structure Of Escherichia Coli Rnase Hi In Complex Wi 2.8 Angstroms Resolution: Proof For A Single Mg2+ Site
authors K.Katayanagi, K.Morikawa
compound source
Molecule: Ribonuclease H
Chain: A
Ec: 3.1.26.4
Engineered: Yes
 Organism_scientific: Escherichia Coli
Organism_taxid: 562
symmetry Space Group: P 43 2 2
R_factor
R_Free NULL
crystal
cell
length a length b length c angle alpha angle beta angle gamma
63.200 63.200 80.600 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.80 Å
ligand MG enzyme Hydrolase E.C.3.1.26.4 BRENDA
related structures by homologous chain: 1RCH, 1WSE
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceCrystal structure of Escherichia coli RNase HI in complex with Mg2+ at 2.8 A resolution: proof for a single Mg(2+)-binding site., Katayanagi K, Okumura M, Morikawa K, Proteins 1993 Dec;17(4):337-46. PMID:8108376
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (30 Kb) [Save to disk]
  • Biological Unit Coordinates (1rdd.pdb1.gz) 25 Kb
  • LPC: Ligand-Protein Contacts for 1RDD
  • CSU: Contacts of Structural Units for 1RDD
  • Likely Quarternary Molecular Structure file(s) for 1RDD
  • Structure Factors (20 Kb)
  • Retrieve 1RDD in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1RDD from S2C, [Save to disk]
  • Re-refined 1rdd structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 1RDD 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 1RDD
  • Ramachandran plot from PDBSum
    • Structure-derived information
  • Electron Density related parameters from EDS Electron Density Server, at Upsala
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 1RDD, from MSDmotif at EBI
  • Genome occurence of 1RDD's fold from GeneCensus
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1rdd__, region [Jmol] [rasmolscript] [script source]
  • 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: [1rdd_A] [1rdd]
  • SWISS-PROT database: [P0A7Y4]
  • Domain organization of [RNH_ECOLI] by SWISSPFAM
    • Other resources with information on 1RDD
  • Community annotation for 1RDD at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
    • Movements, Movies and Images
  • Domain movements in 1RDD from the Database of Macromolecular Movements.
  • Images from IMB Jena Image Library of Biological Macromolecules.

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