4D4C

The catalytic domain, BcGH76, of Bacillus circulans Aman6 in complex with 1,6-ManDMJ

• PDB DOI: https://doi.org/10.2210/pdb4D4C/pdb

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


• Deposited: 2014-10-27 Released: 2015-03-25 
• Deposition Author(s): Thompson, A.J., Speciale, G., Iglesias-Fernandez, J., Hakki, Z., Belz, T., Cartmell, A., Spears, R.J., Stepper, J., Gilbert, H.J., Rovira, C., Williams, S.J., Davies, G.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.30 Å
• R-Value Free: 0.209 
• R-Value Work: 0.175 
• R-Value Observed: 0.177 

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)

Macromolecule Content

• Total Structure Weight: 82.61 kDa 
• Atom Count: 6,225 
• Modelled Residue Count: 671 
• Deposited Residue Count: 724 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ALPHA-1,6-MANNANASE	A, B	362	Niallia circulans	Mutation(s): 1  EC: 3.2.1.101
UniProt
Find proteins for Q9Z4P9 (Niallia circulans) Explore Q9Z4P9  Go to UniProtKB:  Q9Z4P9

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MAN	D [auth A], G [auth B]	alpha-D-mannopyranose C6 H12 O6 WQZGKKKJIJFFOK-PQMKYFCFSA-N
DMJ	C [auth A], F [auth B]	1-DEOXYMANNOJIRIMYCIN C6 H13 N O4 LXBIFEVIBLOUGU-KVTDHHQDSA-N
EDO	E [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.30 Å
• R-Value Free: 0.209 
• R-Value Work: 0.175 
• R-Value Observed: 0.177 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 82.248	α = 90
b = 85.285	β = 90
c = 100.613	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
REFMAC	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-03-25 
Deposition Author(s): Thompson, A.J., Speciale, G., Iglesias-Fernandez, J., Hakki, Z., Belz, T., Cartmell, A., Spears, R.J., Stepper, J., Gilbert, H.J., Rovira, C., Williams, S.J., Davies, G.J.

Revision History  

• Version 1.0: 2015-03-25
  Type: Initial release
  
• Version 1.1: 2015-05-06
  Changes: Database references
• Version 1.2: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Other, Structure summary