6N9M | pdb_00006n9m

Crystal Structure of Adenosine Deaminase from Salmonella typhimurium with Pentostatin (Deoxycoformycin)

• PDB DOI: https://doi.org/10.2210/pdb6N9M/pdb

• Classification: HYDROLASE
• Organism(s): Salmonella enterica subsp. enterica serovar Typhimurium str. LT2
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2018-12-03 Released: 2019-02-06 
• Deposition Author(s): Maltseva, N., Kim, Y., Grimshaw, S., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free: 
  0.168 (Depositor), 0.168 (DCC) 
• R-Value Work: 
  0.154 (Depositor), 0.155 (DCC) 
• R-Value Observed: 
  0.155 (Depositor) 

Literature

Crystal Structure of Adenosine Deaminase from Salmonella typhimurium Complexed with Pentostatin (Deoxycoformycin) (CASP target)

Maltseva, N., Kim, Y., Grimshaw, S., Joachimiak, A.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content 

• Total Structure Weight: 37.98 kDa 
• Atom Count: 2,943 
• Modeled Residue Count: 331 
• Deposited Residue Count: 341 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Adenosine deaminase	A	341	Salmonella enterica subsp. enterica serovar Typhimurium str. LT2	Mutation(s): 0  Gene Names: add, STM1463 EC: 3.5.4.4
UniProt
Find proteins for Q8ZPL9 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)) Explore Q8ZPL9  Go to UniProtKB:  Q8ZPL9

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DCF	B [auth A]	2'-DEOXYCOFORMYCIN C11 H16 N4 O4 FPVKHBSQESCIEP-JQCXWYLXSA-N
ZN	C [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
FMT	F [auth A]	FORMIC ACID C H2 O2 BDAGIHXWWSANSR-UHFFFAOYSA-N
CA	D [auth A], E [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-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: 1.45 Å
• R-Value Free:  0.168 (Depositor), 0.168 (DCC) 
• R-Value Work:  0.154 (Depositor), 0.155 (DCC) 
• R-Value Observed: 0.155 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.081	α = 90
b = 73.232	β = 90
c = 91.875	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-02-06 
Deposition Author(s): Maltseva, N., Kim, Y., Grimshaw, S., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History  

• Version 1.0: 2019-02-06
  Type: Initial release
  
• Version 1.1: 2024-10-16
  Changes: Data collection, Database references, Derived calculations, Structure summary