6D72 | pdb_00006d72

Crystal structure of spermidine/spermine N-acetyltransferase SpeG from Yersinia pestis in complex with calcium ions.

• PDB DOI: https://doi.org/10.2210/pdb6D72/pdb

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


• Deposited: 2018-04-23 Released: 2018-05-16 
• 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: 2.17 Å
• R-Value Free: 
  0.212 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.182 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.183 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of spermidine/spermine N-acetyltransferase SpeG from Yersinia pestis in complex with calcium 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: gel filtration

Macromolecule Content 

• Total Structure Weight: 65.71 kDa 
• Atom Count: 4,683 
• Modeled Residue Count: 523 
• Deposited Residue Count: 552 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Spermidine N1-acetyltransferase	A, B, C	184	Yersinia pestis	Mutation(s): 0  Gene Names: speG, y1405, YP_2698 EC: 2.3.1.57
UniProt
Find proteins for A0A5P8YIA2 (Yersinia pestis) Explore A0A5P8YIA2  Go to UniProtKB:  A0A5P8YIA2

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PEG	F [auth A], H [auth B]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
MLI	G [auth A], I [auth B], K [auth C], L [auth C], M [auth C], N [auth C], O [auth C]	MALONATE ION C3 H2 O4 OFOBLEOULBTSOW-UHFFFAOYSA-L
CA	D [auth A], E [auth A], J [auth C]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.17 Å
• R-Value Free:  0.212 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.182 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.183 (Depositor) 

Diffraction Data: https://doi.org/10.18430/m36d72

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 101.761	α = 90
b = 120.804	β = 90
c = 123.33	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2018-05-16 
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: 2018-05-16
  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