3AFJ | pdb_00003afj

Crystal Structure of Cellvibrio gilvus Cellobiose Phosphorylase triple mutant

• PDB DOI: https://doi.org/10.2210/pdb3AFJ/pdb

• Classification: TRANSFERASE
• Organism(s): Cellulomonas gilvus ATCC 13127
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2010-03-04 Released: 2011-03-23 
• Deposition Author(s): Hidaka, M., Ogawa, N., Fushinobu, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.186 (Depositor), 0.190 (DCC) 
• R-Value Work: 
  0.133 (Depositor), 0.130 (DCC) 
• R-Value Observed: 
  0.136 (Depositor) 

Starting Model: experimental

Literature

Engineering of cellobiose phosphorylase

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

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: 186.66 kDa 
• Atom Count: 15,056 
• 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 ATCC 13127	Mutation(s): 3  EC: 2.4.1.20
UniProt
Find proteins for O66264 (Cellulomonas gilvus) Explore O66264  Go to UniProtKB:  O66264

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BGC	C [auth A], F [auth B]	beta-D-glucopyranose C6 H12 O6 WQZGKKKJIJFFOK-VFUOTHLCSA-N
PO4	D [auth A], G [auth B]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
K	E [auth A], H [auth B]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.186 (Depositor), 0.190 (DCC) 
• R-Value Work:  0.133 (Depositor), 0.130 (DCC) 
• R-Value Observed: 0.136 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 84.137	α = 90
b = 97.963	β = 102.67
c = 104.228	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-03-23 
Deposition Author(s): Hidaka, M., Ogawa, N., Fushinobu, S.

Revision History  

• Version 1.0: 2011-03-23
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Database references, Derived calculations, Structure summary
• Version 1.3: 2023-11-01
  Changes: Data collection, Database references, Refinement description, Structure summary