8QRZ | pdb_00008qrz

Microbacterium testaceum C-glucosyl deglycosidase (CGD), wild type

PDB DOI: https://doi.org/10.2210/pdb8QRZ/pdb

Classification: LYASE
Organism(s): Microbacterium testaceum
Expression System: Escherichia coli B
Mutation(s): No

Deposited: 2023-10-09 Released: 2025-04-23
Deposition Author(s): Furlanetto, V., Kalyani, D.C., Divne, C.
Funding Organization(s): Other government, Other private

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.290 (Depositor), 0.286 (DCC)
R-Value Work:
0.236 (Depositor), 0.236 (DCC)
R-Value Observed:
0.237 (Depositor)

Starting Model: in silico
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This is version 1.0 of the entry. See complete history.

Literature

Microbacterium testaceum C-glucosyl deglycosidase (CGD), wild type

Furlanetto, V., Kalyani, D.C., Srivastava, V., Hallberg, B.M., Ezcurra, I., Divne, C.

To be published.

Macromolecule Content

Total Structure Weight: 195.41 kDa
Atom Count: 14,165
Modeled Residue Count: 1,740
Deposited Residue Count: 1,740
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Sugar phosphate isomerase	A, B, C, D	435	Microbacterium testaceum	Mutation(s): 0 Gene Names: NS220_14145
UniProt
Find proteins for A0A147EV52 (Microbacterium testaceum) Explore A0A147EV52 Go to UniProtKB: A0A147EV52
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A147EV52
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
RB (Subject of Investigation/LOI) Query on RB Download:Ideal Coordinates CCD File SDF format, chain H [auth D] SDF format, chain G [auth C] SDF format, chain F [auth B] SDF format, chain E [auth A] MOL2 format, chain H [auth D] MOL2 format, chain G [auth C] MOL2 format, chain F [auth B] MOL2 format, chain E [auth A] mmCIF format, chain H [auth D] mmCIF format, chain G [auth C] mmCIF format, chain F [auth B] mmCIF format, chain E [auth A]	E [auth A], F [auth B], G [auth C], H [auth D]	RUBIDIUM ION Rb NCCSSGKUIKYAJD-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth C] Focus chain H [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth C] Focus chain H [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.290 (Depositor), 0.286 (DCC)
R-Value Work: 0.236 (Depositor), 0.236 (DCC)
R-Value Observed: 0.237 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.22	α = 90.17
b = 80.41	β = 94.39
c = 82.96	γ = 106.58

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHENIX	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2025-04-23

Deposition Author(s):

Funding Organization	Location	Grant Number
Other government	Sweden	Formas 2017-00983
Other private	Sweden	Oscar and Lili Lamm Memorial Foundation DO2017-0020
Other government	Sweden	VR 2017-03877

Revision History (Full details and data files)

Version 1.0: 2025-04-23
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.