5VMA

Structure of B. pumilus GH48 in complex with a cellobio-derived isofagomine

• PDB DOI: https://doi.org/10.2210/pdb5VMA/pdb

• Classification: HYDROLASE
• Organism(s): Bacillus pumilus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2017-04-27 Released: 2018-10-31 
• Deposition Author(s): Alahuhta, P.M., Lunin, V.V.
• Funding Organization(s): Department of Energy (DOE, United States)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 0.196 
• R-Value Work: 0.154 
• R-Value Observed: 0.156 

Literature

Bacillus pumilus family 48 glycoside hydrolase in complex with cellobio-derived isofagomine

Alahuhta, P.M., Lunin, V.V.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 82.2 kDa 
• Atom Count: 6,480 
• Modelled Residue Count: 700 
• Deposited Residue Count: 709 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycoside hydrolase	A	709	Bacillus pumilus	Mutation(s): 0  Gene Names: BPUM_1559
UniProt
Find proteins for A8FDC4 (Bacillus pumilus (strain SAFR-032)) Explore A8FDC4  Go to UniProtKB:  A8FDC4

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
G2I	B [auth A], C [auth A]	(3R,4R,5R)-3-hydroxy-5-(hydroxymethyl)piperidin-4-yl 4-O-beta-D-glucopyranosyl-beta-D-glucopyranoside C18 H33 N O13 ZIMIYDWQNDRGNF-IONZOCAKSA-N
9MR	D [auth A]	(3R,4R,5R)-3-hydroxy-5-(hydroxymethyl)piperidin-4-yl beta-D-glucopyranoside C12 H23 N O8 LEOSSOWHBSKZSO-WUYFHPBOSA-N
MLI	T [auth A]	MALONATE ION C3 H2 O4 OFOBLEOULBTSOW-UHFFFAOYSA-L
EDO	H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], N [auth A], O [auth A], P [auth A], Q [auth A], R [auth A], S [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
ACT	U [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
CA	E [auth A], F [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
NA	G [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 0.196 
• R-Value Work: 0.154 
• R-Value Observed: 0.156 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 98.891	α = 90
b = 98.891	β = 90
c = 216.799	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PROTEUM PLUS	data collection
PROTEUM PLUS	data processing
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2018-10-31 
Deposition Author(s): Alahuhta, P.M., Lunin, V.V.

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Funding Organization	Location	Grant Number
Department of Energy (DOE, United States)	United States	--

Revision History  

• Version 1.0: 2018-10-31
  Type: Initial release
  
• Version 1.1: 2019-12-04
  Changes: Author supporting evidence
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Derived calculations, Structure summary
• Version 2.1: 2023-10-04
  Changes: Data collection, Database references, Refinement description, Structure summary