5F4S | pdb_00005f4s

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

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.72 Å
  • R-Value Free: 
    0.219 (Depositor), 0.219 (DCC) 
  • R-Value Work: 
    0.180 (Depositor), 0.182 (DCC) 
  • R-Value Observed: 
    0.181 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.2 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.

Macromolecule Content 

  • Total Structure Weight: 147.4 kDa 
  • Atom Count: 11,725 
  • Modeled Residue Count: 1,298 
  • Deposited Residue Count: 1,308 
  • Unique protein chains: 1

Macromolecules

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|  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: lacD2, lacD.2, SPy_1919, M5005_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
P6F

Query on P6F


Download:Ideal Coordinates CCD File
E [auth A]1,6-di-O-phosphono-D-fructose
C6 H14 O12 P2
XPYBSIWDXQFNMH-UYFOZJQFSA-N
13P

Query on 13P


Download:Ideal Coordinates CCD File
F [auth A],
J [auth B]		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 B],
L [auth B],
M [auth C]		CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL

Query on CL


Download:Ideal Coordinates CCD File
G [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.72 Å
  • R-Value Free:  0.219 (Depositor), 0.219 (DCC) 
  • R-Value Work:  0.180 (Depositor), 0.182 (DCC) 
  • R-Value Observed: 0.181 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 64.011α = 90
b = 109.141β = 90
c = 238.335γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

  • Released Date: 2016-12-28 
    • Deposition Author(s): LowKam, C.

Revision History  (Full details and data files)

  • Version 1.0: 2016-12-28
    Type: Initial release
  • Version 1.1: 2023-09-27
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.2: 2024-11-20
    Changes: Structure summary