6D72

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.17 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.183 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


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.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Spermidine N1-acetyltransferase
A, B, C
184Yersinia pestisMutation(s): 0 
Gene Names: speGy1405YP_2698
EC: 2.3.1.57
UniProt
Find proteins for A0A5P8YIA2 (Yersinia pestis)
Explore A0A5P8YIA2 
Go to UniProtKB:  A0A5P8YIA2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A5P8YIA2
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PEG
Query on PEG

Download Ideal Coordinates CCD File 
F [auth A],
H [auth B]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
MLI
Query on MLI

Download Ideal Coordinates CCD File 
G [auth A]
I [auth B]
K [auth C]
L [auth C]
M [auth C]
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
Query on CA

Download Ideal Coordinates CCD File 
D [auth A],
E [auth A],
J [auth C]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 101.761α = 90
b = 120.804β = 90
c = 123.33γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
BLU-MAXdata collection

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


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

Revision History  (Full details and data files)

  • 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