1JI2 Hydrolase date Jun 28, 2001
title Improved X-Ray Structure Of Thermoactinomyces Vulgaris R-47 Amylase 2
authors S.Kamitori, A.Abe, A.Ohtaki, A.Kaji, T.Tonozuka, Y.Sakano
compound source
Molecule: Alpha-Amylase II
Chain: A, B
Synonym: Neopullulanase
Ec: 3.2.1.135
Engineered: Yes
 Organism_scientific: Thermoactinomyces Vulgaris
Organism_taxid: 2026
Strain: R-47
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: P 21 21 21
R_factor 0.179 R_Free 0.224
crystal
cell
length a length b length c angle alpha angle beta angle gamma
112.457 117.684 112.674 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.30 Å
ligand CA enzyme Hydrolase E.C.3.2.1.135 BRENDA
related structures by homologous chain: 1VB9, 1WZK
Gene
Ontology
ChainFunctionProcessComponent
A, B


Primary referenceCrystal structures and structural comparison of Thermoactinomyces vulgaris R-47 alpha-amylase 1 (TVAI) at 1.6 A resolution and alpha-amylase 2 (TVAII) at 2.3 A resolution., Kamitori S, Abe A, Ohtaki A, Kaji A, Tonozuka T, Sakano Y, J Mol Biol. 2002 Apr 26;318(2):443-53. PMID:12051850
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (209 Kb) [Save to disk]
  • Biological Unit Coordinates (1ji2.pdb1.gz) 204 Kb
  • LPC: Ligand-Protein Contacts for 1JI2
  • CSU: Contacts of Structural Units for 1JI2
  • Likely Quarternary Molecular Structure file(s) for 1JI2
  • Structure Factors (520 Kb)
  • Retrieve 1JI2 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1JI2 from S2C, [Save to disk]
  • Re-refined 1ji2 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 1JI2 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 1JI2
  • 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 1JI2, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1ji2a1, region A:1-120 [Jmol] [rasmolscript] [script source]
        - Domain d1ji2a3, region A:121-502 [Jmol] [rasmolscript] [script source]
        - Domain d1ji2a2, region A:503-585 [Jmol] [rasmolscript] [script source]
        - Domain d1ji2b1, region B:1-120 [Jmol] [rasmolscript] [script source]
        - Domain d1ji2b3, region B:121-502 [Jmol] [rasmolscript] [script source]
        - Domain d1ji2b2, region B:503-585 [Jmol] [rasmolscript] [script source]
        - Domain d1q1ji2, region I:114-227 [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: [1ji2_A] [1ji2] [1ji2_B]
  • SWISS-PROT database: [Q08751]
  • Domain organization of [NEPU2_THEVU] by SWISSPFAM
  • Domain found in 1JI2: [Aamy ] by SMART
    • Other resources with information on 1JI2
  • Community annotation for 1JI2 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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