3U4A

From soil to structure: a novel dimeric family 3-beta-glucosidase isolated from compost using metagenomic analysis

• PDB DOI: https://doi.org/10.2210/pdb3U4A/pdb

• Classification: HYDROLASE
• Organism(s): compost metagenome
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2011-10-07 Released: 2013-04-10 
• Deposition Author(s): McAndrew, R.P., Park, J.I., Reindl, W., Friedland, G.D., D'haeseleer, P., Northen, T., Sale, K.L., Simmons, B.A., Adams, P.D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.222 
• R-Value Work: 0.188 
• R-Value Observed: 0.188 

Literature

From soil to structure: a novel dimeric family 3-beta--glucosidase isolated from compost using metagenomic analysis

McAndrew, R.P., Park, J.I., Reindl, W., Friedland, G.D., D'haeseleer, P., Northen, T., Sale, K.L., Simmons, B.A., Adams, P.D.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content

• Total Structure Weight: 172.05 kDa 
• Atom Count: 12,027 
• Modelled Residue Count: 1,481 
• Deposited Residue Count: 1,550 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
JMB19063	A, B	775	compost metagenome	Mutation(s): 0

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-glucopyranose-(1-4)-beta-D-glucopyranose	C, D	2		N/A
Glycosylation Resources
GlyTouCan:  G84824ZO GlyCosmos:  G84824ZO

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BGC	E [auth A], G [auth B]	beta-D-glucopyranose C6 H12 O6 WQZGKKKJIJFFOK-VFUOTHLCSA-N
CA	F [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900005	C, D	beta-cellobiose	Oligosaccharide / Metabolism

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.222 
• R-Value Work: 0.188 
• R-Value Observed: 0.188 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 121.748	α = 90
b = 121.748	β = 90
c = 242.816	γ = 90

Software Package:

Software Name	Purpose
BOS	data collection
PHENIX	model building
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-04-10 
Deposition Author(s): McAndrew, R.P., Park, J.I., Reindl, W., Friedland, G.D., D'haeseleer, P., Northen, T., Sale, K.L., Simmons, B.A., Adams, P.D.

Revision History  

• Version 1.0: 2013-04-10
  Type: Initial release
  
• Version 1.1: 2014-04-02
  Changes: Source and taxonomy
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
• Version 2.1: 2024-02-28
  Changes: Data collection, Database references, Structure summary