7XIH

Crystal structure of the aminopropyltransferase, SpeE from hyperthermophilic crenarchaeon, Pyrobaculum calidifontis in complex with 5'-methylthioadenosine (MTA) and spermidine

  • Classification: TRANSFERASE
  • Organism(s): Pyrobaculum calidifontis JCM 11548
  • Expression System: Escherichia coli
  • Mutation(s): No 

  • Deposited: 2022-04-13 Released: 2022-06-15 
  • Deposition Author(s): Mizohata, E., Yasuda, Y.
  • Funding Organization(s): Japan Science and Technology, Ministry of Education, Culture, Sports, Science and Technology (Japan), New Energy and Industrial Technology Development Organization (NEDO)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.20 Å
  • R-Value Free: 0.154 
  • R-Value Work: 0.119 
  • R-Value Observed: 0.121 

Starting Model: experimental
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This is version 1.1 of the entry. See complete history. 


Literature

Substrate Specificity of an Aminopropyltransferase and the Biosynthesis Pathway of Polyamines in the Hyperthermophilic Crenarchaeon Pyrobaculum calidifontis.

Fukuda, W., Osaki, M., Yasuda, Y., Hidese, R., Higuchi, T., Umezawa, N., Fujiwara, S., Mizohata, E.

(2022) Catalysts 12


Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Polyamine aminopropyltransferase
A, B
309Pyrobaculum calidifontis JCM 11548Mutation(s): 0 
Gene Names: speE, Pcal_0772
EC: 2.5.1.16
UniProt
Find proteins for A3MU81 (Pyrobaculum calidifontis (strain DSM 21063 / JCM 11548 / VA1))
Explore A3MU81 
Go to UniProtKB:  A3MU81
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA3MU81
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.20 Å
  • R-Value Free: 0.154 
  • R-Value Work: 0.119 
  • R-Value Observed: 0.121 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 176.567α = 90
b = 57.256β = 98.5
c = 54.485γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Cootmodel building
Aimlessdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Japan Science and TechnologyJapanJPMJPR17GB
Ministry of Education, Culture, Sports, Science and Technology (Japan)Japan19H05780
New Energy and Industrial Technology Development Organization (NEDO)JapanJPNP18016

Revision History  (Full details and data files)

  • Version 1.0: 2022-06-15
    Type: Initial release
  • Version 1.1: 2023-11-29
    Changes: Data collection, Refinement description