3T81 | pdb_00003t81

Crystal Structure of diiron adenine deaminase

• PDB DOI: https://doi.org/10.2210/pdb3T81/pdb

• Classification: HYDROLASE
• Organism(s): Agrobacterium fabrum str. C58
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2011-08-01 Released: 2011-11-02 
• Deposition Author(s): Bagaria, A., Kumaran, D., Burley, S.K., Swaminathan, S., New York SGX Research Center for Structural Genomics (NYSGXRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.63 Å
• R-Value Free: 
  0.287 (Depositor), 0.284 (DCC) 
• R-Value Work: 
  0.185 (Depositor), 0.186 (DCC) 
• R-Value Observed: 
  0.190 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of diiron adenine deaminase

Bagaria, A., Kumaran, D., Burley, S.K., Swaminathan, S.

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: 130.47 kDa 
• Atom Count: 8,674 
• Modeled Residue Count: 1,166 
• Deposited Residue Count: 1,216 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Adenine deaminase 2	A, B	608	Agrobacterium fabrum str. C58	Mutation(s): 0  Gene Names: ade2, adeC, AGR_L_883, Atu4426 EC: 3.5.4.2
UniProt
Find proteins for Q7CUX4 (Agrobacterium fabrum (strain C58 / ATCC 33970)) Explore Q7CUX4  Go to UniProtKB:  Q7CUX4

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FE	C [auth A], D [auth A], E [auth A], F [auth B], G [auth B], H [auth B]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.63 Å
• R-Value Free:  0.287 (Depositor), 0.284 (DCC) 
• R-Value Work:  0.185 (Depositor), 0.186 (DCC) 
• R-Value Observed: 0.190 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.662	α = 90
b = 131.845	β = 97.04
c = 69.628	γ = 90

Software Package:

Software Name	Purpose
CBASS	data collection
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
REFMAC	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-11-02 
Deposition Author(s): Bagaria, A., Kumaran, D., Burley, S.K., Swaminathan, S., New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History  

• Version 1.0: 2011-11-02
  Type: Initial release
  
• Version 1.1: 2021-02-10
  Changes: Database references, Derived calculations, Structure summary
• Version 1.2: 2023-09-13
  Changes: Data collection, Database references, Refinement description
• Version 1.3: 2023-12-06
  Changes: Data collection
• Version 1.4: 2024-11-20
  Changes: Structure summary