4V40 | pdb_00004v40

BETA-GALACTOSIDASE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Work: 
    0.168 (DCC) 
  • R-Value Observed: 
    0.174 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 4V40

This is version 1.2 of the entry. See complete history

Literature

Three-dimensional structure of beta-galactosidase from E. coli.

Jacobson, R.H.Zhang, X.J.DuBose, R.F.Matthews, B.W.

(1994) Nature 369: 761-766

  • DOI: https://doi.org/10.1038/369761a0
  • Primary Citation Related Structures: 
    4V40

  • PubMed Abstract: 

    The beta-galactosidase from Escherichia coli was instrumental in the development of the operon model, and today is one of the most commonly used enzymes in molecular biology. Here we report the structure of this protein and show that it is a tetramer with 222-point symmetry. The 1,023-amino-acid polypeptide chain folds into five sequential domains, with an extended segment at the amino terminus. The participation of this amino-terminal segment in a subunit interface, coupled with the observation that each active site is made up of elements from two different subunits, provides a structural rationale for the phenomenon of alpha-complementation. The structure represents the longest polypeptide chain for which an atomic structure has been determined. Our results show that it is possible successfully to study non-viral protein crystals with unit cell dimensions in excess of 500 A and with relative molecular masses in the region of 2,000K per asymmetric unit. Non-crystallographic symmetry averaging proved to be a very powerful tool in the structure determination, as has been shown in other contexts.


  • Organizational Affiliation
    • Institute of Molecular Biology, Howard Hughes Medical Institute, University of Oregon, Eugene 97403.

Macromolecule Content 

  • Total Structure Weight: 1,864.29 kDa 
  • Atom Count: 132,654 
  • Modeled Residue Count: 16,336 
  • Deposited Residue Count: 16,368 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
BETA-GALACTOSIDASE
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P
1,023Escherichia coliMutation(s): 0 
EC: 3.2.1.23
UniProt
Find proteins for P00722 (Escherichia coli (strain K12))
Explore P00722 
Go to UniProtKB:  P00722
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00722
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MG

Query on MG



Download:Ideal Coordinates CCD File
AA [auth F]
BA [auth F]
CA [auth G]
DA [auth G]
EA [auth H]
AA [auth F],
BA [auth F],
CA [auth G],
DA [auth G],
EA [auth H],
FA [auth H],
GA [auth I],
HA [auth I],
IA [auth J],
JA [auth J],
KA [auth K],
LA [auth K],
MA [auth L],
NA [auth L],
OA [auth M],
PA [auth N],
Q [auth A],
QA [auth N],
R [auth A],
RA [auth O],
S [auth B],
SA [auth O],
T [auth B],
TA [auth P],
U [auth C],
UA [auth P],
V [auth C],
W [auth D],
X [auth D],
Y [auth E],
Z [auth E]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Work:  0.168 (DCC) 
  • R-Value Observed: 0.174 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 107.9α = 90
b = 207.5β = 94.7
c = 509.9γ = 90
Software Package:
Software NamePurpose
TNTrefinement
TNTrefinement
WEISdata reduction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-07-09
    Type: Initial release
  • Version 1.1: 2014-12-10
    Changes: Other
  • Version 1.2: 2024-02-28
    Changes: Data collection, Database references, Derived calculations, Other