8D32

Mycobacterium tuberculosis pduO-type ATP:cobalamin adenosyltransferase bound to 5-deoxyadenosylrhodibalamin and PPPi

PDB DOI: https://doi.org/10.2210/pdb8D32/pdb

Classification: TRANSFERASE
Organism(s): Mycobacterium tuberculosis
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2022-05-31 Released: 2023-05-10
Deposition Author(s): Mascarenhas, R.N., Ruetz, M., Koutmos, M., Banerjee, R.
Funding Organization(s): National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK), American Heart Association

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.85 Å
R-Value Free: 0.246
R-Value Work: 0.218
R-Value Observed: 0.220

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

A noble substitution leads to the cofactor mimicry by rhodibalamin

Ruetz, M., Mascarenhas, R.N., Koutmos, M., Krautler, B., Banerjee, R.

To be published.

Macromolecule Content

Total Structure Weight: 22.65 kDa
Atom Count: 1,558
Modelled Residue Count: 186
Deposited Residue Count: 193
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Corrinoid adenosyltransferase	A	193	Mycobacterium tuberculosis	Mutation(s): 0 Gene Names: MT1354 EC: 2.5.1.17
UniProt
Find proteins for P9WP99 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WP99 Go to UniProtKB: P9WP99
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P9WP99
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SF0 (Subject of Investigation/LOI) Query on SF0 Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	B [auth A]	[5-(5,6-dimethyl-1H-benzimidazol-1-yl)-4-hydroxy-2-(hydroxymethyl)oxolan-3-yl 1-{3-[3,14,19-tris(2-amino-2-oxoethyl)-8,13,18-tris(3-amino-3-oxopropyl)-1,4,6,9,9,14,16,19-octamethyl-20,21,22,23-tetraazapentacyclo[15.2.1.1~2,5~.1~7,10~.1~12,15~]tricosa-5(23),6,10,12(21),15,17(20)-hexaen-4-yl-kappa~4~N~20~,N~21~,N~22~,N~23~]propanamido}propan-2-yl hydrogenato phosphate]rhodium (non-preferred name) C₆₂ H₈₉ N₁₃ O₁₄ P Rh VWWNYPUYAVYGSM-SSEWGYSZSA-M		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
3PO (Subject of Investigation/LOI) Query on 3PO Download Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A]	D [auth A]	TRIPHOSPHATE H₅ O₁₀ P₃ UNXRWKVEANCORM-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
5AD (Subject of Investigation/LOI) Query on 5AD Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A]	C [auth A]	5'-DEOXYADENOSINE C₁₀ H₁₃ N₅ O₃ XGYIMTFOTBMPFP-KQYNXXCUSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A]	E [auth A], F [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Interactions & Density Focus chain E [auth A] Focus chain F [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.85 Å
R-Value Free: 0.246
R-Value Work: 0.218
R-Value Observed: 0.220
Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.618	α = 90
b = 62.618	β = 90
c = 266.997	γ = 120

Software Package:

Software Name	Purpose
XDS	data reduction
Aimless	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
PHASER	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2023-05-10

Deposition Author(s):

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)	United States	RO1-DK45776
American Heart Association	United States	19POST34370113