4MJ8 | pdb_00004mj8

Crystal structure of spermidine N-acetyltransferase from Vibrio cholerae in complex with polyamine

• PDB DOI: https://doi.org/10.2210/pdb4MJ8/pdb

• Classification: TRANSFERASE
• Organism(s): Vibrio cholerae O1 biovar El Tor str. N16961
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2013-09-03 Released: 2013-09-25 
• Deposition Author(s): Filippova, E.V., Minasov, G., Shuvalova, L., Kiryukhina, O., Kuhn, M.L., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.04 Å
• R-Value Free: 
  0.211 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.169 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.171 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of spermidine N-acetyltransferase from Vibrio cholerae in complex with polyamine

Filippova, E.V., Minasov, G., Shuvalova, L., Kiryukhina, O., Kuhn, M.L., Anderson, W.F.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D6  (Explore in 3D)
Global Stoichiometry: Homo 12-mer - A12 

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

Macromolecule Content 

• Total Structure Weight: 64.01 kDa 
• Atom Count: 4,787 
• Modeled Residue Count: 508 
• Deposited Residue Count: 528 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Spermidine n1-acetyltransferase	A, B, C	176	Vibrio cholerae O1 biovar El Tor str. N16961	Mutation(s): 0  Gene Names: VC_A0947 EC: 2.3.1.57
UniProt
Find proteins for Q9KL03 (Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)) Explore Q9KL03  Go to UniProtKB:  Q9KL03

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SPM	D [auth A], E [auth A], H [auth B], J [auth C]	SPERMINE C10 H26 N4 PFNFFQXMRSDOHW-UHFFFAOYSA-N
EOH	F [auth A], G [auth A], I [auth B], K [auth C], L [auth C], M [auth C]	ETHANOL C2 H6 O LFQSCWFLJHTTHZ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.04 Å
• R-Value Free:  0.211 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.169 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.171 (Depositor) 

Diffraction Data: https://doi.org/10.18430/m34mj8

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.999	α = 90
b = 135.445	β = 90
c = 141.188	γ = 90

Software Package:

Software Name	Purpose
Blu-Ice	data collection
PHASER	phasing
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-09-25 
Deposition Author(s): Filippova, E.V., Minasov, G., Shuvalova, L., Kiryukhina, O., Kuhn, M.L., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History  

• Version 1.0: 2013-09-25
  Type: Initial release
  
• Version 1.1: 2014-03-05
  Changes: Structure summary
• Version 1.2: 2014-03-19
  Changes: Database references
• Version 1.3: 2017-11-15
  Changes: Refinement description
• Version 1.4: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description