1ODZ

Expansion of the glycosynthase repertoire to produce defined manno-oligosaccharides

• PDB DOI: https://doi.org/10.2210/pdb1ODZ/pdb

• Classification: HYDROLASE
• Organism(s): Cellvibrio japonicus
• Expression System: Escherichia coli BL21
• Mutation(s): Yes 


• Deposited: 2003-03-17 Released: 2003-07-10 
• Deposition Author(s): Jahn, M., Stoll, D., Warren, R.A.J., Szabo, L., Singh, P., Gilbert, H.J., Ducros, V.M.A., Davies, G.J., Withers, S.G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free: 0.177 
• R-Value Work: 0.151 
• R-Value Observed: 0.152 

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PQS (software)

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PQS (software)

Macromolecule Content

• Total Structure Weight: 88.46 kDa 
• Atom Count: 7,200 
• Modelled Residue Count: 758 
• Deposited Residue Count: 772 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mannan endo-1,4-beta-mannosidase	A, B	386	Cellvibrio japonicus	Mutation(s): 1  Gene Names: manA, man26A, CJA_2770 EC: 3.2.1.78
UniProt
Find proteins for P49424 (Cellvibrio japonicus (strain Ueda107)) Explore P49424  Go to UniProtKB:  P49424

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-mannopyranose-(1-4)-alpha-D-mannopyranose	C, D	2		N/A
Glycosylation Resources
GlyTouCan:  G78926JO GlyCosmos:  G78926JO GlyGen:  G78926JO

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TRS	F [auth A], I [auth B]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C4 H12 N O3 LENZDBCJOHFCAS-UHFFFAOYSA-O
ZN	E [auth A], H [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
NA	G [auth A], J [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free: 0.177 
• R-Value Work: 0.151 
• R-Value Observed: 0.152 
• Space Group: P 4₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 131.855	α = 90
b = 131.855	β = 90
c = 54.268	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2003-07-10 
Deposition Author(s): Jahn, M., Stoll, D., Warren, R.A.J., Szabo, L., Singh, P., Gilbert, H.J., Ducros, V.M.A., Davies, G.J., Withers, S.G.

Revision History  

• Version 1.0: 2003-07-10
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2018-06-20
  Changes: Data collection, Database references, Source and taxonomy, Structure summary
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Other, Structure summary
• Version 2.1: 2023-12-13
  Changes: Data collection, Database references, Refinement description, Structure summary