1Q6D Hydrolase date Aug 13, 2003
title Crystal Structure Of Soybean Beta-Amylase Mutant (M51t) With Ph Optimum
authors A.Hirata, M.Adachi, A.Sekine, Y.N.Kang, S.Utsumi, B.Mikami
compound source
Molecule: Beta-Amylase
Chain: A
Ec: 3.2.1.2
Engineered: Yes
Mutation: Yes
Organism_scientific: Glycine Max
Organism_common: Soybean
Organism_taxid: 3847
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Jm105
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pkk233-2
symmetry Space Group: P 31 2 1
R_factor 0.177 R_Free 0.215
crystal
cell
length a length b length c angle alpha angle beta angle gamma
86.354 86.354 145.629 90.00 90.00 120.00
method X-Ray Diffractionresolution 2.00 Å
ligand BGC, GLC, SO4 enzyme Hydrolase E.C.3.2.1.2 BRENDA
related structures by homologous chain: 1BFN, 1BTC
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceStructural and enzymatic analysis of soybean beta-amylase mutants with increased pH optimum., Hirata A, Adachi M, Sekine A, Kang YN, Utsumi S, Mikami B, J Biol Chem 2004 Feb 20;279(8):7287-95. Epub 2003 Nov 24. PMID:14638688
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (92 Kb) [Save to disk]
  • Biological Unit Coordinates (1q6d.pdb1.gz) 85 Kb
  • LPC: Ligand-Protein Contacts for 1Q6D
  • CSU: Contacts of Structural Units for 1Q6D
  • Likely Quarternary Molecular Structure file(s) for 1Q6D
  • Structure Factors (503 Kb)
  • Retrieve 1Q6D in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1Q6D from S2C, [Save to disk]
  • Re-refined 1q6d structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1Q6D 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 1Q6D
  • 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 1Q6D, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1q6da_, region A [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: [1q6d] [1q6d_A]
  • SWISS-PROT database: [P10538]
  • Domain organization of [AMYB_SOYBN] by SWISSPFAM
  • Other resources with information on 1Q6D
  • Community annotation for 1Q6D 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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