6CX8 | pdb_00006cx8

Crystal structure of spermidine/spermine N-acetyltransferase SpeG from Vibrio cholerae in complex with manganese ions.

• PDB DOI: https://doi.org/10.2210/pdb6CX8/pdb

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


• Deposited: 2018-04-02 Released: 2018-04-18 
• Deposition Author(s): Filippova, E.V., Minasov, G., Kiryukhina, O., Anderson, W.F., Satchell, K.J.F., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.41 Å
• R-Value Free: 
  0.213 (Depositor), 0.215 (DCC) 
• R-Value Work: 
  0.171 (Depositor), 0.177 (DCC) 
• R-Value Observed: 
  0.173 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of spermidine/spermine N-acetyltransferase SpeG from Vibrio cholerae in complex with manganese ions.

Filippova, E.V., Minasov, G., Kiryukhina, O., Anderson, W.F., Satchell, K.J.F., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

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)

Biological Assembly Evidence: SAXS

Macromolecule Content 

• Total Structure Weight: 126.7 kDa 
• Atom Count: 8,922 
• Modeled Residue Count: 1,020 
• Deposited Residue Count: 1,056 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Spermidine N(1)-acetyltransferase	A, B, C, D, E, F	176	Vibrio cholerae O1 biovar El Tor str. N16961	Mutation(s): 0  Gene Names: speG, 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 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MPD	Q [auth F]	(4S)-2-METHYL-2,4-PENTANEDIOL C6 H14 O2 SVTBMSDMJJWYQN-YFKPBYRVSA-N
PO4	I [auth A], M [auth C], N [auth D], P [auth E]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
IPA	H [auth A], J [auth B], L [auth C]	ISOPROPYL ALCOHOL C3 H8 O KFZMGEQAYNKOFK-UHFFFAOYSA-N
MN	G [auth A], K [auth C], O [auth E]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.41 Å
• R-Value Free:  0.213 (Depositor), 0.215 (DCC) 
• R-Value Work:  0.171 (Depositor), 0.177 (DCC) 
• R-Value Observed: 0.173 (Depositor) 

Diffraction Data: https://doi.org/10.18430/m36cx8

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 157.645	α = 90
b = 135.267	β = 118.58
c = 73.675	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
BLU-MAX	data collection
HKL-3000	data scaling
HKL-3000	data reduction
PHASER	phasing
Coot	model building

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2018-04-18 
Deposition Author(s): Filippova, E.V., Minasov, G., Kiryukhina, O., Anderson, W.F., Satchell, K.J.F., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	--

Revision History  

• Version 1.0: 2018-04-18
  Type: Initial release
  
• Version 1.1: 2019-12-18
  Changes: Author supporting evidence
• Version 1.2: 2023-10-04
  Changes: Data collection, Database references, Derived calculations, Refinement description