7XDQ | pdb_00007xdq

Crystal structure of a glucosylglycerol phosphorylase mutant from Marinobacter adhaerens

PDB DOI: https://doi.org/10.2210/pdb7XDQ/pdb

Classification: BIOSYNTHETIC PROTEIN
Organism(s): Marinobacter adhaerens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2022-03-28 Released: 2023-02-08
Deposition Author(s): Wei, H.L., Li, Q., Yang, J.G., Liu, W.D., Sun, Y.X.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.83 Å
R-Value Free:
0.302 (Depositor), 0.313 (DCC)
R-Value Work:
0.244 (Depositor), 0.277 (DCC)
R-Value Observed:
0.247 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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

Literature

Protein Engineering of Glucosylglycerol Phosphorylase Facilitating Efficient and Highly Regio- and Stereoselective Glycosylation of Polyols in a Synthetic System.

Zhang, T., Liu, P., Wei, H., Sun, X., Zeng, Y., Zhang, X., Cai, Y., Cui, M., Ma, H., Liu, W., Sun, Y., Yang, J.

(2022) ACS Catal : 15715-15727

DOI: https://doi.org/10.1021/acscatal.2c05232

Macromolecule Content

Total Structure Weight: 55.12 kDa
Atom Count: 3,801
Modeled Residue Count: 470
Deposited Residue Count: 480
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glucosylglycerol phosphorylase	A	480	Marinobacter adhaerens	Mutation(s): 9 Gene Names: gtfA, HP15_2853 EC: 2.4.1.359
UniProt
Find proteins for E4PMA5 (Marinobacter adhaerens (strain DSM 23420 / HP15)) Explore E4PMA5 Go to UniProtKB: E4PMA5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	E4PMA5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
BGC (Subject of Investigation/LOI) Query on BGC 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]	beta-D-glucopyranose C₆ H₁₂ O₆ WQZGKKKJIJFFOK-VFUOTHLCSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
LI Query on LI Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	LITHIUM ION Li HBBGRARXTFLTSG-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.83 Å
R-Value Free: 0.302 (Depositor), 0.313 (DCC)
R-Value Work: 0.244 (Depositor), 0.277 (DCC)
R-Value Observed: 0.247 (Depositor)

Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 176.437	α = 90
b = 176.437	β = 90
c = 128.473	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
HKL-2000	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: 2023-02-08

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2023-02-08
Type: Initial release
Version 1.1: 2023-11-29
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.