1Z5U | pdb_00001z5u

Crystal structure of S. typhimurium AphA complexed with cyclic-AMP

• PDB DOI: https://doi.org/10.2210/pdb1Z5U/pdb

• Classification: HYDROLASE
• Organism(s): Salmonella enterica subsp. enterica serovar Typhimurium
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2005-03-20 Released: 2006-03-21 
• Deposition Author(s): Makde, R.D., Kumar, V.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.204 (Depositor), 0.158 (DCC) 
• R-Value Work: 
  0.159 (Depositor), 0.163 (DCC) 

Starting Model: experimental

Literature

Structure and Function of class-B bacterial non-specific acid phosphatase: functional role of invariant Lys154

Makde, R.D., Gupta, G.D., Kumar, V.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Macromolecule Content 

• Total Structure Weight: 96.9 kDa 
• Atom Count: 7,162 
• Modeled Residue Count: 836 
• Deposited Residue Count: 856 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
AphA protein	A, B, C, D	214	Salmonella enterica subsp. enterica serovar Typhimurium	Mutation(s): 0  Gene Names: aphA EC: 3.1.3.2
UniProt
Find proteins for Q540U1 (Salmonella typhimurium) Explore Q540U1  Go to UniProtKB:  Q540U1

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CMP	F [auth A], H [auth B], J [auth C], L [auth D]	ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE C10 H12 N5 O6 P IVOMOUWHDPKRLL-KQYNXXCUSA-N
MG	E [auth A], G [auth B], I [auth C], K [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.204 (Depositor), 0.158 (DCC) 
• R-Value Work:  0.159 (Depositor), 0.163 (DCC) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.71	α = 90
b = 84.3	β = 90
c = 149.83	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
TRUNCATE	data reduction
CNS	refinement
CCP4	data scaling
TRUNCATE	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-03-21 
Deposition Author(s): Makde, R.D., Kumar, V.

Revision History  

• Version 1.0: 2006-03-21
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-10-11
  Changes: Refinement description
• Version 1.4: 2023-10-25
  Changes: Data collection, Database references, Derived calculations, Refinement description