3D2C Hydrolase date May 08, 2008
title Structure Of 4d3, A Thermostable Mutant Of Bacillus Subtilis Obtained Through Directed Evolution
authors R.Sankaranarayanan, M.Z.Kamal
compound source
Molecule: Lipase
Chain: A, B, C, D, E, F, G, H, I, J, K, L
Synonym: Triacylglycerol Lipase
Engineered: Yes
Mutation: Yes
Organism_scientific: Bacillus Subtilis
Organism_taxid: 1423
Gene: Lipa, Lip, Bsu02700
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet21b
symmetry Space Group: C 2 2 21
R_factor 0.202 R_Free 0.245
length a length b length c angle alpha angle beta angle gamma
132.285 198.042 197.902 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.18 Å
enzyme Hydrolase E.C. BRENDA
F, A, J, K, E, B, H, C, D, I, G, L

Primary referenceThermostable Bacillus subtilis lipases: in vitro evolution and structural insight., Ahmad S, Kamal MZ, Sankaranarayanan R, Rao NM, J Mol Biol. 2008 Aug 29;381(2):324-40. Epub 2008 Jul 2. PMID:18599073
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (353 Kb) [Save to disk]
  • Biological Unit Coordinates (3d2c.pdb1.gz) 33 Kb
  • Biological Unit Coordinates (3d2c.pdb2.gz) 33 Kb
  • Biological Unit Coordinates (3d2c.pdb3.gz) 33 Kb
  • Biological Unit Coordinates (3d2c.pdb4.gz) 33 Kb
  • Biological Unit Coordinates (3d2c.pdb5.gz) 33 Kb
  • Biological Unit Coordinates (3d2c.pdb6.gz) 33 Kb
  • Biological Unit Coordinates (3d2c.pdb7.gz) 33 Kb
  • Biological Unit Coordinates (3d2c.pdb8.gz) 33 Kb
  • Biological Unit Coordinates (3d2c.pdb9.gz) 33 Kb
  • CSU: Contacts of Structural Units for 3D2C
  • Likely Quarternary Molecular Structure file(s) for 3D2C
  • Structure Factors (1098 Kb)
  • Retrieve 3D2C in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3D2C from S2C, [Save to disk]
  • Re-refined 3d2c structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3D2C 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 3D2C
  • Cartoon representation from PDB Cartoon
  • 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
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 3D2C, from MSDmotif at EBI
  • Fold representative 3d2c from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3d2c_A] [3d2c_L] [3d2c_B] [3d2c_G] [3d2c_F] [3d2c_D] [3d2c] [3d2c_H] [3d2c_J] [3d2c_I] [3d2c_E] [3d2c_C] [3d2c_K]
  • SWISS-PROT database: [P37957]
  • Domain organization of [ESTA_BACSU] by SWISSPFAM
  • Other resources with information on 3D2C
  • Community annotation for 3D2C 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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