9VGA | pdb_00009vga

Crystal structure of Phaeodactylibacter sp. phosphoglucomutase in complex with manganese ion

PDB DOI: https://doi.org/10.2210/pdb9VGA/pdb

Classification: ISOMERASE
Organism(s): Phaeodactylibacter sp.
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2025-06-13 Released: 2026-05-13
Deposition Author(s): Shen, Y.W., Tu, T.
Funding Organization(s): Other government, National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.82 Å
R-Value Free:
0.310 (Depositor), 0.308 (DCC)
R-Value Work:
0.249 (Depositor), 0.249 (DCC)
R-Value Observed:
0.252 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.0 of the entry. See complete history.

Literature

In Vitro Design and Optimization of a High-Efficiency Artificial Enzymatic Pathway for Cellulose-to-Starch Conversion

Shen, Y.W., Tu, T.

To be published.

Macromolecule Content

Total Structure Weight: 59.56 kDa
Atom Count: 4,478
Modeled Residue Count: 545
Deposited Residue Count: 546
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphoglucomutase (Alpha-D-glucose-1,6-bisphosphate-dependent)	A	546	Phaeodactylibacter sp.	Mutation(s): 0 Gene Names: pgm, KDD09_20305 EC: 5.4.2.2
UniProt
Find proteins for A0A2D0NJ94 (Flavilitoribacter nigricans (strain ATCC 23147 / DSM 23189 / NBRC 102662 / NCIMB 1420 / SS-2)) Explore A0A2D0NJ94 Go to UniProtKB: A0A2D0NJ94
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A2D0NJ94
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MN (Subject of Investigation/LOI) Query on MN Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.82 Å
R-Value Free: 0.310 (Depositor), 0.308 (DCC)
R-Value Work: 0.249 (Depositor), 0.249 (DCC)
R-Value Observed: 0.252 (Depositor)

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.657	α = 90
b = 101.706	β = 90
c = 168.361	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2026-05-13

Deposition Author(s):

Funding Organization	Location	Grant Number
Other government	China	2022YFA0912301
National Natural Science Foundation of China (NSFC)	China	U25A20709

Revision History (Full details and data files)

Version 1.0: 2026-05-13
Type: Initial release

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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.