3KAO | pdb_00003kao

Crystal structure of tagatose 1,6-diphosphate aldolase from Staphylococcus aureus

• PDB DOI: https://doi.org/10.2210/pdb3KAO/pdb

• Classification: LYASE
• Organism(s): Staphylococcus aureus subsp. aureus Mu50
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2009-10-19 Released: 2009-10-27 
• Deposition Author(s): Chang, C., Marshall, N., Cobb, G., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.171 (Depositor), 0.183 (DCC) 
• R-Value Work: 
  0.148 (Depositor), 0.163 (DCC) 
• R-Value Observed: 
  0.149 (Depositor) 

Literature

Crystal structure of tagatose 1,6-diphosphate aldolase from Staphylococcus aureus

Chang, C., Marshall, N., Cobb, G., Joachimiak, A.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 37.91 kDa 
• Atom Count: 3,204 
• Modeled Residue Count: 325 
• Deposited Residue Count: 329 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tagatose 1,6-diphosphate aldolase	A	329	Staphylococcus aureus subsp. aureus Mu50	Mutation(s): 0  Gene Names: lacD, SAV2192, Staphylococcus aureus subsp. aureus Mu50 EC: 4.1.2.40
UniProt
Find proteins for P0A009 (Staphylococcus aureus (strain Mu50 / ATCC 700699)) Explore P0A009  Go to UniProtKB:  P0A009

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	B [auth A], C [auth A], H [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	G [auth A], I [auth A], J [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN	D [auth A], E [auth A], F [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.171 (Depositor), 0.183 (DCC) 
• R-Value Work:  0.148 (Depositor), 0.163 (DCC) 
• R-Value Observed: 0.149 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 84.704	α = 90
b = 84.704	β = 90
c = 202.759	γ = 90

Software Package:

Software Name	Purpose
SBC-Collect	data collection
HKL-3000	phasing
SHELXD	phasing
SHELXE	model building
MLPHARE	phasing
DM	model building
RESOLVE	model building
Coot	model building
ARP/wARP	model building
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
DM	phasing
RESOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-10-27 
Deposition Author(s): Chang, C., Marshall, N., Cobb, G., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2009-10-27
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2017-11-01
  Changes: Refinement description
• Version 1.3: 2024-11-20
  Changes: Data collection, Database references, Derived calculations, Structure summary