7QOQ | pdb_00007qoq

Crystal structure of Mycobacterium hassiacum glucosyl-3-phosphoglycerate synthase at pH 8.5 in complex with UMP and Magnesium

PDB DOI: https://doi.org/10.2210/pdb7QOQ/pdb

Classification: TRANSFERASE
Organism(s): Mycolicibacterium hassiacum DSM 44199
Expression System: Escherichia coli BL21
Mutation(s): No

Deposited: 2021-12-27 Released: 2023-01-18
Deposition Author(s): Silva, A., Barbosa Pereira, P.J., Macedo-Ribeiro, S., Costa, D.
Funding Organization(s): Fundacao para a Ciencia e a Tecnologia

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.93 Å
R-Value Free:
0.228 (Depositor), 0.228 (DCC)
R-Value Work:
0.176 (Depositor), 0.176 (DCC)
R-Value Observed:
0.178 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.0 of the entry. See complete history.

Literature

Crystal structure of Mycobacterium hassiacum glucosyl-3-phosphoglycerate synthase at pH 8.5 in complex with UMP and Magnesium

Silva, A., Nunes-Costa, D., Empadinhas, N., Barbosa Pereira, P.J., Macedo-Ribeiro, S.

To be published.

Macromolecule Content

Total Structure Weight: 71.08 kDa
Atom Count: 5,070
Modeled Residue Count: 593
Deposited Residue Count: 654
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glucosyl-3-phosphoglycerate synthase	A, B	327	Mycolicibacterium hassiacum DSM 44199	Mutation(s): 0 Gene Names: gpgS, C731_3243, MHAS_02845 EC: 2.4.1.266
UniProt
Find proteins for K5B7Z4 (Mycolicibacterium hassiacum (strain DSM 44199 / CIP 105218 / JCM 12690 / 3849)) Explore K5B7Z4 Go to UniProtKB: K5B7Z4
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	K5B7Z4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
U5P (Subject of Investigation/LOI) Query on U5P Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain H [auth B] MOL2 format, chain D [auth A] MOL2 format, chain H [auth B] mmCIF format, chain D [auth A] mmCIF format, chain H [auth B]	D [auth A], H [auth B]	URIDINE-5'-MONOPHOSPHATE C₉ H₁₃ N₂ O₉ P DJJCXFVJDGTHFX-XVFCMESISA-N		Interactions Focus chain D [auth A] Focus chain H [auth B] Interactions & Density Focus chain D [auth A] Focus chain H [auth B]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain F [auth A] SDF format, chain G [auth B] SDF format, chain I [auth B] MOL2 format, chain C [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth B] MOL2 format, chain I [auth B] mmCIF format, chain C [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth B] mmCIF format, chain I [auth B]	C [auth A], F [auth A], G [auth B], I [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain F [auth A] Focus chain G [auth B] Focus chain I [auth B] Interactions & Density Focus chain C [auth A] Focus chain F [auth A] Focus chain G [auth B] Focus chain I [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.93 Å
R-Value Free: 0.228 (Depositor), 0.228 (DCC)
R-Value Work: 0.176 (Depositor), 0.176 (DCC)
R-Value Observed: 0.178 (Depositor)

Diffraction Data:

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.076	α = 90
b = 90.377	β = 90
c = 96.007	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2023-01-18

Deposition Author(s):

Silva, A.

Barbosa Pereira, P.J.

Macedo-Ribeiro, S.

Costa, D.

Funding Organization	Location	Grant Number
Fundacao para a Ciencia e a Tecnologia	Portugal	PTDC/BTM-TEC/29221/2017 (POCI-01-0145-FEDER-029221).

Revision History (Full details and data files)

Version 1.0: 2023-01-18
Type: Initial release
Version 1.1: 2023-03-01
Changes: Database references, Structure summary
Version 1.2: 2024-02-07
Changes: Data collection, Refinement description
Version 2.0: 2025-12-17
Changes: Atomic model, Author supporting evidence, Data collection, Derived calculations, Non-polymer description, Structure summary