4DCA | pdb_00004dca

Crystal structure of aminoglycoside phosphotransferase APH(2'')-Ib, ADP-bound

• PDB DOI: https://doi.org/10.2210/pdb4DCA/pdb
• Entry: 4DCA supersedes: 3R70

• Classification: TRANSFERASE
• Organism(s): Escherichia coli
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2012-01-17 Released: 2012-02-01 
• Deposition Author(s): Stogios, P.J., Minasov, G., Singer, A.U., Tan, K., Nocek, B., Evdokimova, E., Egorova, O., Di Leo, R., Savchenko, A., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.225 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.195 (Depositor), 0.192 (DCC) 
• R-Value Observed: 
  0.197 (Depositor) 

Literature

Crystal structure of aminoglycoside phosphotransferase APH(2'')-Ib, ADP-bound

Stogios, P.J., Minasov, G., Singer, A.U., Tan, K., Nocek, B., Evdokimova, E., Egorova, O., Di Leo, R., Savchenko, A., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

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: 38.61 kDa 
• Atom Count: 2,885 
• Modelled Residue Count: 296 
• Deposited Residue Count: 320 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Aminoglycoside phosphotransferase	A	320	Escherichia coli	Mutation(s): 0  Gene Names: aph(2')-Ib
UniProt
Find proteins for Q93ET9 (Escherichia coli) Explore Q93ET9  Go to UniProtKB:  Q93ET9

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ADP	B [auth A]	ADENOSINE-5'-DIPHOSPHATE C10 H15 N5 O10 P2 XTWYTFMLZFPYCI-KQYNXXCUSA-N
MG	C [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-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: 1.80 Å
• R-Value Free:  0.225 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.195 (Depositor), 0.192 (DCC) 
• R-Value Observed: 0.197 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.938	α = 90
b = 88.465	β = 90
c = 62.299	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
SHELXS	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-02-01 
Deposition Author(s): Stogios, P.J., Minasov, G., Singer, A.U., Tan, K., Nocek, B., Evdokimova, E., Egorova, O., Di Leo, R., Savchenko, A., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)
• This entry supersedes: 3R70

Revision History  

• Version 1.0: 2012-02-01
  Type: Initial release
  
• Version 1.1: 2024-11-20
  Changes: Data collection, Database references, Derived calculations, Structure summary