5F4W

Tagatose-1,6-bisphosphate aldolase from Streptococcus pyogenes in complex with TBP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.66 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.174 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

NON-STEREOSPECIFIC SUBSTRATE CLEAVAGE BY TAGATOSE-BISPHOSPHATE CLASS I ALDOLASE

LowKam, C.Liotard, B.Sygusch, J.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Tagatose 1,6-diphosphate aldolase 2
A, B, C, D
327Streptococcus pyogenes serotype M1Mutation(s): 0 
Gene Names: lacD2lacD.2SPy_1919M5005_Spy1635
EC: 4.1.2.40
UniProt
Find proteins for P63705 (Streptococcus pyogenes serotype M1)
Explore P63705 
Go to UniProtKB:  P63705
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP63705
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
P6T
Query on P6T

Download Ideal Coordinates CCD File 
E [auth A]1,6-di-O-phosphono-D-tagatose
C6 H14 O12 P2
XPYBSIWDXQFNMH-PQLUHFTBSA-N
13P
Query on 13P

Download Ideal Coordinates CCD File 
G [auth A]1,3-DIHYDROXYACETONEPHOSPHATE
C3 H7 O6 P
GNGACRATGGDKBX-UHFFFAOYSA-N
CA
Query on CA

Download Ideal Coordinates CCD File 
H [auth A],
I [auth A],
K [auth C],
M [auth D]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
F [auth A],
J [auth B],
L [auth C],
N [auth D]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.66 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.174 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 63.955α = 90
b = 107.373β = 90
c = 237.73γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

  • Released Date: 2017-02-01 
  • Deposition Author(s): LowKam, C.

Revision History  (Full details and data files)

  • Version 1.0: 2017-02-01
    Type: Initial release
  • Version 1.1: 2023-09-27
    Changes: Data collection, Database references, Derived calculations, Refinement description