4RE3 | pdb_00004re3

Different transition state conformations for the hydrolysis of beta-mannosides and beta-glucosides in the rice Os7BGlu26 family GH1 beta-mannosidase/beta-glucosidase

• PDB DOI: https://doi.org/10.2210/pdb4RE3/pdb

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


• Deposited: 2014-09-21 Released: 2015-09-16 
• Deposition Author(s): Tankrathok, A., Iglesias-Fernandez, J., Williams, R.J., Hakki, Z., Robinson, R.C., Hrmova, M., Rovira, C., Williams, S.J., Ketudat Cairns, J.R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.55 Å
• R-Value Free: 
  0.213 (Depositor), 0.196 (DCC) 
• R-Value Work: 
  0.175 (Depositor), 0.164 (DCC) 
• R-Value Observed: 
  0.177 (Depositor) 

Starting Model: experimental

Literature

A Single Glycosidase Harnesses Different Pyranoside Ring Transition State Conformations for Hydrolysis of Mannosides and Glucosides

Tankrathok, A., Iglesias-Fernandez, J., Williams, R.J., Pengthaisong, S., Baiya, S., Hakki, Z., Robinson, R.C., Hrmova, M., Rovira, C., Williams, S.J., Ketudat Cairns, J.R.

(2015) ACS Catal 5: 6041-6051

• DOI: https://doi.org/10.1021/acscatal.5b01547

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: 58.63 kDa 
• Atom Count: 4,170 
• Modeled Residue Count: 483 
• 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 (PDB Primary Data), 3.2.1.21 (UniProt)
UniProt
Find proteins for A2YPH1 (Oryza sativa subsp. indica) Explore A2YPH1  Go to UniProtKB:  A2YPH1

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EPE	F [auth A]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C8 H18 N2 O4 S JKMHFZQWWAIEOD-UHFFFAOYSA-N
GIM	H [auth A]	GLUCOIMIDAZOLE C8 H13 N2 O4 RZRDQZQPTISYKY-MVIOUDGNSA-O
TRS	E [auth A]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C4 H12 N O3 LENZDBCJOHFCAS-UHFFFAOYSA-O
GOL	B [auth A], C [auth A], D [auth A], G [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.55 Å
• R-Value Free:  0.213 (Depositor), 0.196 (DCC) 
• R-Value Work:  0.175 (Depositor), 0.164 (DCC) 
• R-Value Observed: 0.177 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.1	α = 90
b = 73.209	β = 90
c = 134.047	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: 2015-09-16 
Deposition Author(s): Tankrathok, A., Iglesias-Fernandez, J., Williams, R.J., Hakki, Z., Robinson, R.C., Hrmova, M., Rovira, C., Williams, S.J., Ketudat Cairns, J.R.

Revision History  

• Version 1.0: 2015-09-16
  Type: Initial release
  
• Version 1.1: 2015-09-23
  Changes: Database references
• Version 1.2: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.3: 2024-10-30
  Changes: Structure summary