7XIG

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

PDB DOI: https://doi.org/10.2210/pdb7XIG/pdb

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: 0.207
R-Value Work: 0.173
R-Value Observed: 0.174

Starting Model: experimental
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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

DOI: https://doi.org/10.3390/catal12050567

Macromolecule Content

Total Structure Weight: 283.35 kDa
Atom Count: 19,343
Modelled Residue Count: 2,294
Deposited Residue Count: 2,472
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Polyamine aminopropyltransferase	A, B, C, D, E A, B, C, D, E, F, G, H	309	Pyrobaculum calidifontis	Mutation(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 Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A3MU81
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MTA (Subject of Investigation/LOI) Query on MTA Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain L [auth B] SDF format, chain N [auth C] SDF format, chain P [auth D] SDF format, chain T [auth F] SDF format, chain V [auth G] SDF format, chain Y [auth H] SDF format, chain R [auth E] MOL2 format, chain I [auth A] MOL2 format, chain L [auth B] MOL2 format, chain N [auth C] MOL2 format, chain P [auth D] MOL2 format, chain T [auth F] MOL2 format, chain V [auth G] MOL2 format, chain Y [auth H] MOL2 format, chain R [auth E] mmCIF format, chain I [auth A] mmCIF format, chain L [auth B] mmCIF format, chain N [auth C] mmCIF format, chain P [auth D] mmCIF format, chain T [auth F] mmCIF format, chain V [auth G] mmCIF format, chain Y [auth H] mmCIF format, chain R [auth E]	I [auth A] L [auth B] N [auth C] P [auth D] R [auth E] I [auth A], L [auth B], N [auth C], P [auth D], R [auth E], T [auth F], V [auth G], Y [auth H]	5'-DEOXY-5'-METHYLTHIOADENOSINE C₁₁ H₁₅ N₅ O₃ S WUUGFSXJNOTRMR-IOSLPCCCSA-N		Interactions Focus chain I [auth A] Focus chain L [auth B] Focus chain N [auth C] Focus chain P [auth D] Focus chain R [auth E] Focus chain T [auth F] Focus chain V [auth G] Focus chain Y [auth H] Interactions & Density Focus chain I [auth A] Focus chain L [auth B] Focus chain N [auth C] Focus chain P [auth D] Focus chain R [auth E] Focus chain T [auth F] Focus chain V [auth G] Focus chain Y [auth H]
EPE (Subject of Investigation/LOI) Query on EPE Download Ideal Coordinates CCD File SDF format, chain K [auth A] SDF format, chain X [auth G] MOL2 format, chain K [auth A] MOL2 format, chain X [auth G] mmCIF format, chain K [auth A] mmCIF format, chain X [auth G]	K [auth A], X [auth G]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C₈ H₁₈ N₂ O₄ S JKMHFZQWWAIEOD-UHFFFAOYSA-N		Interactions Focus chain K [auth A] Focus chain X [auth G] Interactions & Density Focus chain K [auth A] Focus chain X [auth G]
SPM (Subject of Investigation/LOI) Query on SPM Download Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain M [auth B] SDF format, chain O [auth C] SDF format, chain S [auth E] SDF format, chain U [auth F] SDF format, chain W [auth G] SDF format, chain Z [auth H] SDF format, chain Q [auth D] MOL2 format, chain J [auth A] MOL2 format, chain M [auth B] MOL2 format, chain O [auth C] MOL2 format, chain S [auth E] MOL2 format, chain U [auth F] MOL2 format, chain W [auth G] MOL2 format, chain Z [auth H] MOL2 format, chain Q [auth D] mmCIF format, chain J [auth A] mmCIF format, chain M [auth B] mmCIF format, chain O [auth C] mmCIF format, chain S [auth E] mmCIF format, chain U [auth F] mmCIF format, chain W [auth G] mmCIF format, chain Z [auth H] mmCIF format, chain Q [auth D]	J [auth A] M [auth B] O [auth C] Q [auth D] S [auth E] J [auth A], M [auth B], O [auth C], Q [auth D], S [auth E], U [auth F], W [auth G], Z [auth H]	SPERMINE C₁₀ H₂₆ N₄ PFNFFQXMRSDOHW-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Focus chain M [auth B] Focus chain O [auth C] Focus chain Q [auth D] Focus chain S [auth E] Focus chain U [auth F] Focus chain W [auth G] Focus chain Z [auth H] Interactions & Density Focus chain J [auth A] Focus chain M [auth B] Focus chain O [auth C] Focus chain Q [auth D] Focus chain S [auth E] Focus chain U [auth F] Focus chain W [auth G] Focus chain Z [auth H]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.25 Å
R-Value Free: 0.207
R-Value Work: 0.173
R-Value Observed: 0.174
Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.828	α = 72.46
b = 80.392	β = 89.13
c = 97.844	γ = 88.08

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Coot	model building
Aimless	data scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2022-06-15

Deposition Author(s):

Mizohata, E.

Yasuda, Y.

Funding Organization	Location	Grant Number
Japan Science and Technology	Japan	JPMJPR17GB
Ministry of Education, Culture, Sports, Science and Technology (Japan)	Japan	19H05780
New Energy and Industrial Technology Development Organization (NEDO)	Japan	JPNP18016