4BOJ | pdb_00004boj

Crystal structure of Bacillus circulans TN-31 Aman6 in complex with mannobiose

• PDB DOI: https://doi.org/10.2210/pdb4BOJ/pdb

• Classification: HYDROLASE
• Organism(s): Niallia circulans
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2013-05-21 Released: 2014-05-28 
• Deposition Author(s): Striebeck, A., van Aalten, D.M.F.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.38 Å
• R-Value Free: 
  0.191 (Depositor), 0.190 (DCC) 
• R-Value Work: 
  0.171 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.172 (Depositor) 

Literature

The Structure of B. Circulans Aman6 Defines the Fold and Mechanism of the Gh-76 Mannoprotein Transglycosylases and Bacterial Mannosidases

Striebeck, A., Borodkin, V.S., Ferenbach, A.T., Van Aalten, D.M.F.

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 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

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

Biological assembly 3 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 117.56 kDa 
• Atom Count: 9,247 
• Modeled Residue Count: 1,010 
• Deposited Residue Count: 1,032 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ALPHA-1,6-MANNANASE	A, B, C	344	Niallia circulans	Mutation(s): 1
UniProt
Find proteins for Q9Z4P9 (Niallia circulans) Explore Q9Z4P9  Go to UniProtKB:  Q9Z4P9

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose	D, E, F	2		N/A
Glycosylation Resources
GlyTouCan:  G77384RA GlyCosmos:  G77384RA GlyGen:  G77384RA

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900118	D, E, F	6alpha-alpha-mannobiose	Oligosaccharide / Metabolism

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.38 Å
• R-Value Free:  0.191 (Depositor), 0.190 (DCC) 
• R-Value Work:  0.171 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.172 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.63	α = 90
b = 114.14	β = 90
c = 134.41	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-05-28 
Deposition Author(s): Striebeck, A., van Aalten, D.M.F.

Revision History  

• Version 1.0: 2014-05-28
  Type: Initial release
  
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Other, Structure summary
• Version 2.1: 2024-05-08
  Changes: Data collection, Database references, Structure summary