4JIE

Structural analysis and insights into glycon specificity of the rice GH1 Os7BGlu26 beta-D-mannosidase

• PDB DOI: https://doi.org/10.2210/pdb4JIE/pdb

• Classification: HYDROLASE
• Organism(s): Oryza sativa Indica Group
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2013-03-05 Released: 2013-10-09 
• Deposition Author(s): Tankrathok, A., Luang, S., Robinson, R.C., Kimura, A., Hrmova, M., Ketudat Cairns, J.R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.45 Å
• R-Value Free: 0.195 
• R-Value Work: 0.153 
• R-Value Observed: 0.155 

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 58.75 kDa 
• Atom Count: 4,269 
• Modelled Residue Count: 484 
• Deposited Residue Count: 503 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-mannosidase/beta-glucosidase	A	503	Oryza sativa Indica Group	Mutation(s): 0  EC: 3.2.1.25
UniProt
Find proteins for A2YPH1 (Oryza sativa subsp. indica) Explore A2YPH1  Go to UniProtKB:  A2YPH1

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EPE	H [auth A]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C8 H18 N2 O4 S JKMHFZQWWAIEOD-UHFFFAOYSA-N
BMA	I [auth A]	beta-D-mannopyranose C6 H12 O6 WQZGKKKJIJFFOK-RWOPYEJCSA-N
GOL	B [auth A], C [auth A], D [auth A], E [auth A], F [auth A], G [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.45 Å
• R-Value Free: 0.195 
• R-Value Work: 0.153 
• R-Value Observed: 0.155 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.01	α = 90
b = 73.624	β = 90
c = 133.984	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: 2013-10-09 
Deposition Author(s): Tankrathok, A., Luang, S., Robinson, R.C., Kimura, A., Hrmova, M., Ketudat Cairns, J.R.

Revision History  

• Version 1.0: 2013-10-09
  Type: Initial release
  
• Version 1.1: 2014-04-23
  Changes: Database references
• Version 1.2: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Database references, Derived calculations, Structure summary
• Version 1.3: 2023-11-08
  Changes: Data collection, Database references, Refinement description, Structure summary