7P5O | pdb_00007p5o

Crystal structure of Aspergillus fumigatus phosphoglucomutase in complex with the reaction intermediate

PDB DOI: https://doi.org/10.2210/pdb7P5O/pdb

Classification: ISOMERASE
Organism(s): Aspergillus fumigatus
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2021-07-14 Released: 2022-07-27
Deposition Author(s): Raimi, O.G., Yan, K., van Aalten, D.M.F.
Funding Organization(s): Medical Research Council (MRC, United Kingdom)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.48 Å
R-Value Free:
0.258 (Depositor), 0.260 (DCC)
R-Value Work:
0.201 (Depositor), 0.206 (DCC)
R-Value Observed:
0.204 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment

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

Literature

Targeting an essential step in the biosynthetic pathway of uridine diphosphate glucose in Aspergillus fumigatus

Yan, K., Stanley, M., Kowalski, B., Raimi, O.G., Ferenbach, A.T., Wei, P.Z., Yuan, H., Fang, W., van Aalten, D.M.F.

To be published.

Macromolecule Content

Total Structure Weight: 122.69 kDa
Atom Count: 9,110
Modeled Residue Count: 1,114
Deposited Residue Count: 1,120
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphoglucomutase	A, B	560	Aspergillus fumigatus	Mutation(s): 0 Gene Names: CDV57_06471 EC: 5.4.2.2
UniProt
Find proteins for Q4WY53 (Aspergillus fumigatus (strain ATCC MYA-4609 / CBS 101355 / FGSC A1100 / Af293)) Explore Q4WY53 Go to UniProtKB: Q4WY53
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q4WY53
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
G16 (Subject of Investigation/LOI) Query on G16 Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain E [auth B] MOL2 format, chain C [auth A] MOL2 format, chain E [auth B] mmCIF format, chain C [auth A] mmCIF format, chain E [auth B]	C [auth A], E [auth B]	1,6-di-O-phosphono-alpha-D-glucopyranose C₆ H₁₃ O₁₂ P₂ RWHOZGRAXYWRNX-VFUOTHLCSA-M		Interactions Focus chain C [auth A] Focus chain E [auth B] Interactions & Density Focus chain C [auth A] Focus chain E [auth B]
MG (Subject of Investigation/LOI) Query on MG Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain F [auth B] MOL2 format, chain D [auth A] MOL2 format, chain F [auth B] mmCIF format, chain D [auth A] mmCIF format, chain F [auth B]	D [auth A], F [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain F [auth B] Interactions & Density Focus chain D [auth A] Focus chain F [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.48 Å
R-Value Free: 0.258 (Depositor), 0.260 (DCC)
R-Value Work: 0.201 (Depositor), 0.206 (DCC)
R-Value Observed: 0.204 (Depositor)

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 98.57	α = 90
b = 209.61	β = 90
c = 61.2	γ = 90

Software Package:

Software Name	Purpose
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
autoPROC	data reduction
autoPROC	data scaling

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2022-07-27

Deposition Author(s):

van Aalten, D.M.F.

Funding Organization	Location	Grant Number
Medical Research Council (MRC, United Kingdom)	United Kingdom	V001094

Revision History (Full details and data files)

Version 1.0: 2022-07-27
Type: Initial release
Version 1.1: 2024-01-31
Changes: Data collection, Refinement description

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.