2YHG

Ab initio phasing of a nucleoside hydrolase-related hypothetical protein from Saccharophagus degradans that is associated with carbohydrate metabolism

• PDB DOI: https://doi.org/10.2210/pdb2YHG/pdb

• Classification: HYDROLASE
• Organism(s): Saccharophagus degradans 2-40
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2011-04-30 Released: 2011-08-03 
• Deposition Author(s): Hehemann, J.H., Marsters, C., Boraston, A.B.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.08 Å
• R-Value Free: 0.151 
• R-Value Work: 0.133 
• R-Value Observed: 0.134 

Literature

Ab initio phasing of a nucleoside hydrolase-related hypothetical protein from Saccharophagus degradans that is associated with carbohydrate metabolism.

Hehemann, J.H., Marsters, C., Boraston, A.B.

(2011) Proteins 79: 2992-2998

• PubMed: 21905122 
• DOI: https://doi.org/10.1002/prot.23126
• Primary Citation of Related Structures:  
  2YHG

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Organizational Affiliation: 

Biochemistry & Microbiology, University of Victoria, Victoria, BC, Canada.

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 48.26 kDa 
• Atom Count: 3,729 
• Modelled Residue Count: 411 
• Deposited Residue Count: 437 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CELLULOSE-BINDING PROTEIN	A	437	Saccharophagus degradans 2-40	Mutation(s): 0
UniProt
Find proteins for Q21PD3 (Saccharophagus degradans (strain 2-40 / ATCC 43961 / DSM 17024)) Explore Q21PD3  Go to UniProtKB:  Q21PD3

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BTB	M [auth A]	2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C8 H19 N O5 OWMVSZAMULFTJU-UHFFFAOYSA-N
ZN	I [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO	J [auth A], K [auth A], L [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
CA	B [auth A], D [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL	C [auth A], H [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG	E [auth A], F [auth A], G [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.08 Å
• R-Value Free: 0.151 
• R-Value Work: 0.133 
• R-Value Observed: 0.134 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.58	α = 90
b = 61.58	β = 90
c = 125.46	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
iMOSFLM	data reduction
SCALA	data scaling
ACORN	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-08-03 
Deposition Author(s): Hehemann, J.H., Marsters, C., Boraston, A.B.

Revision History  

• Version 1.0: 2011-08-03
  Type: Initial release
  
• Version 1.1: 2011-09-21
  Changes: Database references
• Version 1.2: 2018-06-13
  Changes: Advisory, Data collection, Database references