3S4D | pdb_00003s4d

Lactose phosphorylase in a ternary complex with cellobiose and sulfate

• PDB DOI: https://doi.org/10.2210/pdb3S4D/pdb

• Classification: TRANSFERASE
• Organism(s): Cellulomonas uda
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2011-05-19 Released: 2012-06-27 
• Deposition Author(s): Van Hoorebeke, A., Stout, J., Soetaert, W., Van Beeumen, J., Desmet, T., Savvides, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.30 Å
• R-Value Free: 
  0.340 (Depositor), 0.262 (DCC) 
• R-Value Work: 
  0.296 (Depositor), 0.293 (DCC) 
• R-Value Observed: 
  0.297 (Depositor) 

Literature

Cellobiose phosphorylase: reconstructing the structural itinerary along the catalytic pathway

Van Hoorebeke, A., Stout, J., Soetaert, W., Van Beeumen, J., Desmet, T., Savvides, S.

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: 91.94 kDa 
• Atom Count: 6,328 
• Modeled Residue Count: 822 
• Deposited Residue Count: 822 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lactose Phosphorylase	A	822	Cellulomonas uda	Mutation(s): 2  EC: 2.4.1.20
UniProt
Find proteins for Q7WTR6 (Cellulomonas uda) Explore Q7WTR6  Go to UniProtKB:  Q7WTR6

Oligosaccharides

Help  

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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	C [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Biologically Interesting Molecules (External Reference) 

1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900005	B	beta-cellobiose	Oligosaccharide / Metabolism

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.30 Å
• R-Value Free:  0.340 (Depositor), 0.262 (DCC) 
• R-Value Work:  0.296 (Depositor), 0.293 (DCC) 
• R-Value Observed: 0.297 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 84.71	α = 90
b = 92.88	β = 90
c = 104.42	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data scaling
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-06-27 
Deposition Author(s): Van Hoorebeke, A., Stout, J., Soetaert, W., Van Beeumen, J., Desmet, T., Savvides, S.

Revision History  

• Version 1.0: 2012-06-27
  Type: Initial release
  
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Structure summary
• Version 2.1: 2024-02-28
  Changes: Advisory, Data collection, Database references, Structure summary