3K3S | pdb_00003k3s

Crystal structure of altronate hydrolase (fragment 1-84) from Shigella Flexneri.

• PDB DOI: https://doi.org/10.2210/pdb3K3S/pdb

• Classification: HYDROLASE
• Organism(s): Shigella flexneri 2a str. 2457T
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2009-10-04 Released: 2009-10-27 
• Deposition Author(s): Hou, J., Chruszcz, M., Xu, X., Le, B., Zimmerman, M.D., Savchenko, A., Edwards, A.M., Joachimiak, A., Minor, W., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free: 
  0.213 (Depositor), 0.225 (DCC) 
• R-Value Work: 
  0.174 (Depositor), 0.188 (DCC) 
• R-Value Observed: 
  0.176 (Depositor) 

Literature

Crystal structure of altronate hydrolase (fragment 1-84) from Shigella Flexneri.

Hou, J., Chruszcz, M., Xu, X., Le, B., Zimmerman, M.D., Savchenko, A., Edwards, A.M., Joachimiak, A., Minor, W.

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)

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

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

Biological assembly 3 assigned by authors and generated by PISA (software)

Biological Assembly 4  

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

Biological assembly 4 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 92.9 kDa 
• Atom Count: 5,750 
• Modeled Residue Count: 679 
• Deposited Residue Count: 840 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Altronate hydrolase	A, B, C, D, E, F, G, H	105	Shigella flexneri 2a str. 2457T	Mutation(s): 0  Gene Names: S3338, SF3131, uxaA
UniProt
Find proteins for A0A0H2VY20 (Shigella flexneri) Explore A0A0H2VY20  Go to UniProtKB:  A0A0H2VY20

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MLA	I [auth A], M [auth D]	MALONIC ACID C3 H4 O4 OFOBLEOULBTSOW-UHFFFAOYSA-N
ACT	J [auth B], L [auth C], N [auth E], O [auth F], Q [auth G], S [auth H]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
CL	K [auth B], P [auth G], R [auth H]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B, C, D, E, F, G, H	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free:  0.213 (Depositor), 0.225 (DCC) 
• R-Value Work:  0.174 (Depositor), 0.188 (DCC) 
• R-Value Observed: 0.176 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 113.968	α = 90
b = 40.218	β = 104.33
c = 121.001	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
HKL-3000	phasing
MLPHARE	phasing
DM	model building
SHELXD	phasing
RESOLVE	model building
REFMAC	refinement
HKL-2000	data reduction
HKL-3000	data scaling
DM	phasing
RESOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-10-27 
Deposition Author(s): Hou, J., Chruszcz, M., Xu, X., Le, B., Zimmerman, M.D., Savchenko, A., Edwards, A.M., Joachimiak, A., Minor, W., 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: 2015-04-29
  Changes: Non-polymer description
• Version 1.3: 2022-04-13
  Changes: Database references, Derived calculations, Structure summary
• Version 1.4: 2024-11-20
  Changes: Data collection, Structure summary