8YIF | pdb_00008yif

Crystal structure of GH13_30 alpha-glucosidase CmmB in complex with acarviosin

PDB DOI: https://doi.org/10.2210/pdb8YIF/pdb

Classification: HYDROLASE
Organism(s): Arthrobacter globiformis
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2024-02-29 Released: 2024-07-03
Deposition Author(s): Saburi, W., Tagami, T., Yu, J., Ose, T., Yao, M., Mori, H.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free:
0.196 (Depositor), 0.196 (DCC)
R-Value Work:
0.171 (Depositor), 0.171 (DCC)
R-Value Observed:
0.171 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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Literature

Molecular mechanism for the substrate specificity of Arthrobacter globiformis M6 alpha-glucosidase CmmB, belonging to glycoside hydrolase family 13 subfamily 30

Saburi, W., Tagami, T., Usui, T., Yu, J., Ose, T., Yao, M., Mori, H.

(2024) Food Biosci 61: 104516

DOI: https://doi.org/10.1016/j.fbio.2024.104516

Macromolecule Content

Total Structure Weight: 64.5 kDa
Atom Count: 4,680
Modeled Residue Count: 537
Deposited Residue Count: 575
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Alpha-glucosidase	A	575	Arthrobacter globiformis	Mutation(s): 0 Gene Names: cmmB
UniProt
Find proteins for D2YYD7 (Arthrobacter globiformis) Explore D2YYD7 Go to UniProtKB: D2YYD7
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	D2YYD7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1L2I (Subject of Investigation/LOI) Query on A1L2I 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]	Acarviosin C₁₄ H₂₅ N O₈ KFHKERRGDZTZQJ-SHCNSHNESA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free: 0.196 (Depositor), 0.196 (DCC)
R-Value Work: 0.171 (Depositor), 0.171 (DCC)
R-Value Observed: 0.171 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.223	α = 90
b = 73.336	β = 90.47
c = 73.213	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	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: 2024-07-03

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2024-07-03
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.