Experimental Data Snapshot

  • Resolution: 2.70 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.174 

Starting Model: experimental
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This is version 1.4 of the entry. See complete history


Crystal structures and mechanism of 6-phospho-beta-galactosidase from Lactococcus lactis.

Wiesmann, C.Hengstenberg, W.Schulz, G.E.

(1997) J Mol Biol 269: 851-860

  • DOI: https://doi.org/10.1006/jmbi.1997.1084
  • Primary Citation of Related Structures:  
    2PBG, 3PBG, 4PBG

  • PubMed Abstract: 

    The initial structural model of 6-phospho-beta-galactosidase from Lactococcus lactis was refined to an R-factor of 16.4% (R[free] = 23.6%) to 2.3 A resolution (1 A = 0.1 nm), and the structures of three other crystal forms were solved by molecular replacement. The four structural models are essentially identical. The catalytic center of the enzyme is approximately at the mass center of the molecule and can only be reached through a 20 A long channel, which is observed with an "open" or "closed" entrance. The closed entrance is probably too small for the educt lactose-6-phosphate to enter, but large enough for the first product glucose to leave. Among the presented structures is a complex between an almost inactive mutant and the second product galactose-6-phosphate, which is exclusively bound at side-chains. A superposition (onto the native enzyme) of galactose-6-phosphate as bound to the mutant suggests the geometry of a postulated covalent intermediate. The binding mode of the educt was modeled, starting from the bound galactose-6-phosphate. A tightly fixed tryptophan is used as a chopping-board for splitting the disaccharide, and several other aromatic residues in the active center cavity are likely to participate in substrate transport/binding.

  • Organizational Affiliation

    Institut für Organische Chemie und Biochemie, Albert-Ludwigs-Universität, Freiburg im Breisgau, Germany.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B
468Lactococcus lactisMutation(s): 0 
Gene Names: LACG
Find proteins for P11546 (Lactococcus lactis subsp. lactis)
Explore P11546 
Go to UniProtKB:  P11546
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP11546
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.70 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.174 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 107.1α = 90
b = 174.5β = 90
c = 61γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
MERGEdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1997-07-23
    Type: Initial release
  • Version 1.1: 2008-03-25
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-08-09
    Changes: Database references, Derived calculations, Refinement description
  • Version 1.4: 2024-05-22
    Changes: Data collection