7F82 | pdb_00007f82

Structure of the bacterial cellulose synthase subunit Z in complex with cellooligosaccharides from Enterobacter sp. CJF-002

• PDB DOI: https://doi.org/10.2210/pdb7F82/pdb

• Classification: HYDROLASE
• Organism(s): Enterobacter sp. CJF-002
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2021-06-30 Released: 2022-02-09 
• Deposition Author(s): Fujiwara, T., Fujishima, A., Yao, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.30 Å
• R-Value Free: 
  0.187 (Depositor), 0.171 (DCC) 
• R-Value Work: 
  0.169 (Depositor), 0.171 (DCC) 
• R-Value Observed: 
  0.170 (Depositor) 

Starting Model: experimental

Literature

Structural snapshot of a glycoside hydrolase family 8 endo-beta-1,4-glucanase capturing the state after cleavage of the scissile bond.

Fujiwara, T., Fujishima, A., Nakamura, Y., Tajima, K., Yao, M.

(2022) Acta Crystallogr D Biol Crystallogr 78: 228-237

• DOI: https://doi.org/10.1107/S2059798321012882

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

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 assigned by authors and generated by PISA (software)

Biological Assembly 4  

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

Biological assembly 4 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 162.92 kDa 
• Atom Count: 12,518 
• Modeled Residue Count: 1,352 
• Deposited Residue Count: 1,404 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glucanase	A, B, C, D	351	Enterobacter sp. CJF-002	Mutation(s): 1  Gene Names: bcsZ EC: 3.2.1
UniProt
Find proteins for K0IUV6 (Enterobacter sp. CJF-002) Explore K0IUV6  Go to UniProtKB:  K0IUV6

Oligosaccharides

Help  

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

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose	F, K, N	3		N/A
Glycosylation Resources
GlyTouCan: G14338VK GlyCosmos: G14338VK GlyGen: G14338VK

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose	G, I, L	4		N/A
Glycosylation Resources
GlyTouCan: G00025MO GlyCosmos: G00025MO GlyGen: G00025MO

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SRT	O [auth C], P [auth D]	S,R MESO-TARTARIC ACID C4 H6 O6 FEWJPZIEWOKRBE-XIXRPRMCSA-N

Biologically Interesting Molecules (External Reference) 

3 Unique

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

Entity ID: 3
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900021	F, K, N	beta-cellotriose	Oligosaccharide / Metabolism

Entity ID: 4
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900011	G, I, L	beta-cellotetraose	Oligosaccharide / Metabolism

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.30 Å
• R-Value Free:  0.187 (Depositor), 0.171 (DCC) 
• R-Value Work:  0.169 (Depositor), 0.171 (DCC) 
• R-Value Observed: 0.170 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 89.28	α = 90
b = 92.86	β = 98.41
c = 90.5	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2022-02-09 
Deposition Author(s): Fujiwara, T., Fujishima, A., Yao, M.

Revision History  

• Version 1.0: 2022-02-09
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Data collection, Refinement description