7XDR

Crystal structure of a glucosylglycerol phosphorylase from Marinobacter adhaerens

PDB DOI: https://doi.org/10.2210/pdb7XDR/pdb

Classification: BIOSYNTHETIC PROTEIN
Organism(s): Marinobacter adhaerens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

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: 2.40 Å
R-Value Free: 0.237
R-Value Work: 0.194
R-Value Observed: 0.196

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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: 987.89 kDa
Atom Count: 71,196
Modelled Residue Count: 8,638
Deposited Residue Count: 8,640
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glucosylglycerol phosphorylase	A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R	480	Marinobacter adhaerens	Mutation(s): 0 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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	E4PMA5
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.237
R-Value Work: 0.194
R-Value Observed: 0.196
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 102.267	α = 90
b = 185.174	β = 101.56
c = 257.619	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XSCALE	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
PHASER	phasing

Structure Validation

View Full Validation Report

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

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 R01GM133198.