3QFZ | pdb_00003qfz

Crystal Structure of Cellvibrio gilvus Cellobiose Phosphorylase Complexed with Sulfate and 1-Deoxynojirimycin

• PDB DOI: https://doi.org/10.2210/pdb3QFZ/pdb

• Classification: TRANSFERASE/TRANSFERASE INHIBITOR
• Organism(s): Cellulomonas gilvus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2011-01-24 Released: 2011-09-21 
• Deposition Author(s): Fushinobu, S., Hidaka, M., Hayashi, A.M., Wakagi, T., Shoun, H., Kitaoka, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.39 Å
• R-Value Free: 
  0.208 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.141 (Depositor), 0.150 (DCC) 
• R-Value Observed: 
  0.144 (Depositor) 

Literature

Interactions between glycoside hydrolase family 94 cellobiose phosphorylase and glucosidase inhibitors

Fushinobu, S., Hidaka, M., Hayashi, A.M., Wakagi, T., Shoun, H., Kitaoka, M.

(2011) J Appl Glycosci (1999) 58: 91-97

• DOI: https://doi.org/10.5458/jag.jag.JAG-2010_022

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: 187.55 kDa 
• Atom Count: 13,721 
• Modeled Residue Count: 1,644 
• Deposited Residue Count: 1,684 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cellobiose Phosphorylase	A, B	842	Cellulomonas gilvus	Mutation(s): 0  EC: 2.4.1.20
UniProt
Find proteins for O66264 (Cellulomonas gilvus) Explore O66264  Go to UniProtKB:  O66264

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EPE	F [auth A]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C8 H18 N2 O4 S JKMHFZQWWAIEOD-UHFFFAOYSA-N
BGC	C [auth A], I [auth B]	beta-D-glucopyranose C6 H12 O6 WQZGKKKJIJFFOK-VFUOTHLCSA-N
NOJ	E [auth A], K [auth B]	1-DEOXYNOJIRIMYCIN C6 H13 N O4 LXBIFEVIBLOUGU-JGWLITMVSA-N
SO4	D [auth A], G [auth A], H [auth A], J [auth B], L [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.39 Å
• R-Value Free:  0.208 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.141 (Depositor), 0.150 (DCC) 
• R-Value Observed: 0.144 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 84.906	α = 90
b = 98.128	β = 102.53
c = 104.778	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-09-21 
Deposition Author(s): Fushinobu, S., Hidaka, M., Hayashi, A.M., Wakagi, T., Shoun, H., Kitaoka, M.

Revision History  

• Version 1.0: 2011-09-21
  Type: Initial release
  
• Version 1.1: 2017-11-08
  Changes: Refinement description
• Version 1.2: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Database references, Derived calculations, Structure summary
• Version 1.3: 2024-03-20
  Changes: Data collection, Database references, Structure summary