7XIF

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

PDB DOI: https://doi.org/10.2210/pdb7XIF/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: 2.14 Å
R-Value Free: 0.190
R-Value Work: 0.160
R-Value Observed: 0.162

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: 423.22 kDa
Atom Count: 28,933
Modelled Residue Count: 3,434
Deposited Residue Count: 3,708
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, I, J, K, L	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 S [auth D] SDF format, chain AA [auth H] SDF format, chain CA [auth I] SDF format, chain DA [auth J] SDF format, chain EA [auth K] SDF format, chain FA [auth L] SDF format, chain M [auth A] SDF format, chain O [auth B] SDF format, chain Q [auth C] SDF format, chain U [auth E] SDF format, chain W [auth F] SDF format, chain Y [auth G] MOL2 format, chain S [auth D] MOL2 format, chain AA [auth H] MOL2 format, chain CA [auth I] MOL2 format, chain DA [auth J] MOL2 format, chain EA [auth K] MOL2 format, chain FA [auth L] MOL2 format, chain M [auth A] MOL2 format, chain O [auth B] MOL2 format, chain Q [auth C] MOL2 format, chain U [auth E] MOL2 format, chain W [auth F] MOL2 format, chain Y [auth G] mmCIF format, chain S [auth D] mmCIF format, chain AA [auth H] mmCIF format, chain CA [auth I] mmCIF format, chain DA [auth J] mmCIF format, chain EA [auth K] mmCIF format, chain FA [auth L] mmCIF format, chain M [auth A] mmCIF format, chain O [auth B] mmCIF format, chain Q [auth C] mmCIF format, chain U [auth E] mmCIF format, chain W [auth F] mmCIF format, chain Y [auth G]	AA [auth H] CA [auth I] DA [auth J] EA [auth K] FA [auth L] AA [auth H], CA [auth I], DA [auth J], EA [auth K], FA [auth L], M [auth A], O [auth B], Q [auth C], S [auth D], U [auth E], W [auth F], Y [auth G]	5'-DEOXY-5'-METHYLTHIOADENOSINE C₁₁ H₁₅ N₅ O₃ S WUUGFSXJNOTRMR-IOSLPCCCSA-N		Interactions Focus chain AA [auth H] Focus chain CA [auth I] Focus chain DA [auth J] Focus chain EA [auth K] Focus chain FA [auth L] Focus chain M [auth A] Focus chain O [auth B] Focus chain Q [auth C] Focus chain S [auth D] Focus chain U [auth E] Focus chain W [auth F] Focus chain Y [auth G] Interactions & Density Focus chain AA [auth H] Focus chain CA [auth I] Focus chain DA [auth J] Focus chain EA [auth K] Focus chain FA [auth L] Focus chain M [auth A] Focus chain O [auth B] Focus chain Q [auth C] Focus chain S [auth D] Focus chain U [auth E] Focus chain W [auth F] Focus chain Y [auth G]
TER (Subject of Investigation/LOI) Query on TER Download Ideal Coordinates CCD File SDF format, chain Z [auth G] SDF format, chain V [auth E] SDF format, chain X [auth F] MOL2 format, chain Z [auth G] MOL2 format, chain V [auth E] MOL2 format, chain X [auth F] mmCIF format, chain Z [auth G] mmCIF format, chain V [auth E] mmCIF format, chain X [auth F]	V [auth E], X [auth F], Z [auth G]	N-(3-AMINO-PROPYL)-N-(5-AMINOPROPYL)-1,4-DIAMINOBUTANE C₁₀ H₂₆ N₄ DODDBCGMRAFLEB-UHFFFAOYSA-N		Interactions Focus chain V [auth E] Focus chain X [auth F] Focus chain Z [auth G] Interactions & Density Focus chain V [auth E] Focus chain X [auth F] Focus chain Z [auth G]
SPD (Subject of Investigation/LOI) Query on SPD Download Ideal Coordinates CCD File SDF format, chain BA [auth H] SDF format, chain N [auth A] SDF format, chain R [auth C] SDF format, chain P [auth B] SDF format, chain T [auth D] MOL2 format, chain BA [auth H] MOL2 format, chain N [auth A] MOL2 format, chain R [auth C] MOL2 format, chain P [auth B] MOL2 format, chain T [auth D] mmCIF format, chain BA [auth H] mmCIF format, chain N [auth A] mmCIF format, chain R [auth C] mmCIF format, chain P [auth B] mmCIF format, chain T [auth D]	BA [auth H], N [auth A], P [auth B], R [auth C], T [auth D]	SPERMIDINE C₇ H₁₉ N₃ ATHGHQPFGPMSJY-UHFFFAOYSA-N		Interactions Focus chain BA [auth H] Focus chain N [auth A] Focus chain P [auth B] Focus chain R [auth C] Focus chain T [auth D] Interactions & Density Focus chain BA [auth H] Focus chain N [auth A] Focus chain P [auth B] Focus chain R [auth C] Focus chain T [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.14 Å
R-Value Free: 0.190
R-Value Work: 0.160
R-Value Observed: 0.162
Space Group: P 3₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 166.159	α = 90
b = 166.159	β = 90
c = 149.586	γ = 120

Software Package:

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

Structure Validation

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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