7XII

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

  • Classification: TRANSFERASE
  • Organism(s): Pyrobaculum calidifontis
  • 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: 2.25 Å
  • R-Value Free: 0.170 
  • R-Value Work: 0.149 
  • R-Value Observed: 0.150 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


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
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Polyamine aminopropyltransferase
A, B, C, D
309Pyrobaculum calidifontisMutation(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
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MTA (Subject of Investigation/LOI)
Query on MTA
Download Ideal Coordinates CCD File 
E [auth A],
H [auth B],
J [auth C],
L [auth D]		5'-DEOXY-5'-METHYLTHIOADENOSINE
C11 H15 N5 O3 S
WUUGFSXJNOTRMR-IOSLPCCCSA-N
EPE (Subject of Investigation/LOI)
Query on EPE
Download Ideal Coordinates CCD File 
G [auth A]4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
C8 H18 N2 O4 S
JKMHFZQWWAIEOD-UHFFFAOYSA-N
AG3 (Subject of Investigation/LOI)
Query on AG3
Download Ideal Coordinates CCD File 
F [auth A],
I [auth B],
K [auth C],
M [auth D]		1-{4-[(3-aminopropyl)amino]butyl}guanidine
C8 H21 N5
XYCUJKFFVBCJEF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.170 
  • R-Value Work: 0.149 
  • R-Value Observed: 0.150 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 55.163α = 77.19
b = 57.173β = 78.32
c = 97.308γ = 88.49
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