1GT7

L-rhamnulose-1-phosphate aldolase from Escherichia coli


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.233 

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This is version 1.4 of the entry. See complete history


Literature

The Structure of L-Rhamnulose-1-Phosphate Aldolase (Class II) Solved by Low-Resolution Sir Phasing and 20-Fold Ncs Averaging

Kroemer, M.Schulz, G.E.

(2002) Acta Crystallogr D Biol Crystallogr 58: 824

  • DOI: https://doi.org/10.1107/s0907444902004614
  • Primary Citation of Related Structures:  
    1GT7

  • PubMed Abstract: 

    The enzyme L-rhamnulose-1-phosphate aldolase catalyzes the reversible cleavage of L-rhamnulose-1-phosphate to dihydroxyacetone phosphate and L-lactaldehyde. It is a homotetramer with an M(r) of 30 000 per subunit and crystallized in space group P3(2)21. The enzyme shows a low sequence identity of 18% with the structurally known L-fuculose-1-phosphate aldolase that splits a stereoisomer in a similar reaction. Structure analysis was initiated with a single heavy-atom derivative measured to 6 A resolution. The resulting poor electron density, a self-rotation function and the working hypothesis that both enzymes are C(4) symmetric with envelopes that resemble one another allowed the location of the 20 protomers of the asymmetric unit. The crystal-packing unit was a D(4)-symmetric propeller consisting of five D(4)-symmetric octamers around an internal crystallographic twofold axis. Presumably, the propellers associate laterally in layers, which in turn pile up along the 3(2) axis to form the crystal. The non-crystallographic symmetry was used to extend the phases to the 2.7 A resolution limit and to establish a refined atomic model of the enzyme. The structure showed that the two enzymes are indeed homologous and that they possess chemically similar active centres.


  • Organizational Affiliation

    Institut für Organische Chemie und Biochemie, Albert-Ludwigs-Universität Freiburg, Albertstrasse 21, 79104 Freiburg im Breisgau, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
RHAMNULOSE-1-PHOSPHATE ALDOLASE
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T
274Escherichia coliMutation(s): 0 
EC: 4.1.2.19
UniProt
Find proteins for P32169 (Escherichia coli (strain K12))
Explore P32169 
Go to UniProtKB:  P32169
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP32169
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PGH
Query on PGH

Download Ideal Coordinates CCD File 
BA [auth D]
BB [auth Q]
DA [auth E]
DB [auth R]
FA [auth F]
BA [auth D],
BB [auth Q],
DA [auth E],
DB [auth R],
FA [auth F],
FB [auth S],
HA [auth G],
HB [auth T],
JA [auth H],
LA [auth I],
NA [auth J],
PA [auth K],
RA [auth L],
TA [auth M],
V [auth A],
VA [auth N],
X [auth B],
XA [auth O],
Z [auth C],
ZA [auth P]
PHOSPHOGLYCOLOHYDROXAMIC ACID
C2 H6 N O6 P
BAXHHWZKQZIJID-UHFFFAOYSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
AA [auth D]
AB [auth Q]
CA [auth E]
CB [auth R]
EA [auth F]
AA [auth D],
AB [auth Q],
CA [auth E],
CB [auth R],
EA [auth F],
EB [auth S],
GA [auth G],
GB [auth T],
IA [auth H],
KA [auth I],
MA [auth J],
OA [auth K],
QA [auth L],
SA [auth M],
U [auth A],
UA [auth N],
W [auth B],
WA [auth O],
Y [auth C],
YA [auth P]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.233 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 225.76α = 90
b = 225.76β = 90
c = 285.645γ = 120
Software Package:
Software NamePurpose
DMmodel building
SCALAdata scaling
SCALEITphasing
MLPHAREphasing
GETAXphasing
DMphasing
REFMACrefinement

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2002-05-03
    Type: Initial release
  • Version 1.1: 2013-11-20
    Changes: Derived calculations, Non-polymer description, Other, Version format compliance
  • Version 1.2: 2019-05-08
    Changes: Data collection, Experimental preparation, Other
  • Version 1.3: 2019-07-24
    Changes: Data collection
  • Version 1.4: 2024-05-08
    Changes: Data collection, Database references, Derived calculations, Other