8PNO | pdb_00008pno

The MgF3(H2O) transition state analog complex of E. coli YihX

PDB DOI: https://doi.org/10.2210/pdb8PNO/pdb

Classification: HYDROLASE
Organism(s): Escherichia coli
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2023-06-30 Released: 2024-07-10
Deposition Author(s): Baumann, P., Zappala, D., Jin, Y.
Funding Organization(s): Wellcome Trust

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free:
0.257 (Depositor), 0.266 (DCC)
R-Value Work:
0.212 (Depositor), 0.223 (DCC)
R-Value Observed:
0.214 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 8PNO

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

Literature

The MgF3(H2O)- transition state analog complex of E. coli YihX

Baumann, P., Zappala, D., Jin, Y.

To be published.

Macromolecule Content

Total Structure Weight: 47.48 kDa
Atom Count: 3,539
Modeled Residue Count: 401
Deposited Residue Count: 404
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Alpha-D-glucose 1-phosphate phosphatase YihX	A, B	202	Escherichia coli	Mutation(s): 0 Gene Names: yihX, b3885, JW5566 EC: 3.1.3.10
UniProt
Find proteins for P0A8Y3 (Escherichia coli (strain K12)) Explore P0A8Y3 Go to UniProtKB: P0A8Y3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0A8Y3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 8 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PG4 Query on PG4 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]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain O [auth B] SDF format, chain C [auth A] MOL2 format, chain O [auth B] MOL2 format, chain C [auth A] mmCIF format, chain O [auth B] mmCIF format, chain C [auth A]	C [auth A], O [auth B]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain O [auth B] Interactions & Density Focus chain C [auth A] Focus chain O [auth B]
KQB (Subject of Investigation/LOI) Query on KQB Download:Ideal Coordinates CCD File SDF format, chain M [auth B] SDF format, chain D [auth A] MOL2 format, chain M [auth B] MOL2 format, chain D [auth A] mmCIF format, chain M [auth B] mmCIF format, chain D [auth A]	D [auth A], M [auth B]	trifluoromagnesate monohydrate F₃ H₂ Mg O QUJZUQVZXBKESK-UHFFFAOYSA-K		Interactions Focus chain D [auth A] Focus chain M [auth B] Interactions & Density Focus chain D [auth A] Focus chain M [auth B]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain L [auth B] SDF format, chain J [auth A] SDF format, chain I [auth A] MOL2 format, chain L [auth B] MOL2 format, chain J [auth A] MOL2 format, chain I [auth A] mmCIF format, chain L [auth B] mmCIF format, chain J [auth A] mmCIF format, chain I [auth A]	I [auth A], J [auth A], L [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain J [auth A] Focus chain L [auth B] Interactions & Density Focus chain I [auth A] Focus chain J [auth A] Focus chain L [auth B]
IMD Query on IMD Download:Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	F [auth A]	IMIDAZOLE C₃ H₅ N₂ RAXXELZNTBOGNW-UHFFFAOYSA-O		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain N [auth B] SDF format, chain G [auth A] MOL2 format, chain N [auth B] MOL2 format, chain G [auth A] mmCIF format, chain N [auth B] mmCIF format, chain G [auth A]	G [auth A], N [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain N [auth B] Interactions & Density Focus chain G [auth A] Focus chain N [auth B]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain Q [auth B] SDF format, chain K [auth A] MOL2 format, chain Q [auth B] MOL2 format, chain K [auth A] mmCIF format, chain Q [auth B] mmCIF format, chain K [auth A]	K [auth A], Q [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain K [auth A] Focus chain Q [auth B] Interactions & Density Focus chain K [auth A] Focus chain Q [auth B]
MG (Subject of Investigation/LOI) Query on MG Download:Ideal Coordinates CCD File SDF format, chain P [auth B] SDF format, chain H [auth A] MOL2 format, chain P [auth B] MOL2 format, chain H [auth A] mmCIF format, chain P [auth B] mmCIF format, chain H [auth A]	H [auth A], P [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain P [auth B] Interactions & Density Focus chain H [auth A] Focus chain P [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.257 (Depositor), 0.266 (DCC)
R-Value Work: 0.212 (Depositor), 0.223 (DCC)
R-Value Observed: 0.214 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.259	α = 90
b = 79.325	β = 108.52
c = 80.297	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
xia2	data reduction
Aimless	data scaling
MOLREP	phasing

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2024-07-10

Deposition Author(s):

Funding Organization	Location	Grant Number
Wellcome Trust	United Kingdom	--

Revision History (Full details and data files)

Version 1.0: 2024-07-10
Type: Initial release
Version 1.1: 2024-11-13
Changes: Structure summary
Version 2.0: 2025-11-19
Changes: Non-polymer description, Structure summary

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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.