3SCV | pdb_00003scv

Crystal Structure of Rice BGlu1 E386G/S334A Mutant Complexed with Cellotetraose

• PDB DOI: https://doi.org/10.2210/pdb3SCV/pdb

• Classification: HYDROLASE
• Organism(s): Oryza sativa Japonica Group
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2011-06-08 Released: 2012-02-15 
• Deposition Author(s): Pengthaisong, S., Withers, S.G., Kuaprasert, B., Ketudat Cairns, J.R.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.11 Å
• R-Value Free: 
  0.206 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.173 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.174 (Depositor) 

Starting Model: experimental

Literature

Structural investigation of the basis for cellooligosaccharide synthesis by rice BGlu1 glycosynthases

Pengthaisong, S., Withers, S.G., Kuaprasert, B., Ketudat Cairns, J.R.

To be published.

Biological Assembly 1  

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

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

Biological Assembly 2  

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

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

Macromolecule Content 

• Total Structure Weight: 111.93 kDa 
• Atom Count: 8,557 
• Modeled Residue Count: 944 
• Deposited Residue Count: 962 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-glucosidase 7	A, B	481	Oryza sativa Japonica Group	Mutation(s): 2  Gene Names: BGLU1, BGLU7, LOC_Os03g49600, Os03g0703000, os3bglu7, OSJNBa0004L11.16 EC: 3.2.1.21
UniProt
Find proteins for Q75I93 (Oryza sativa subsp. japonica) Explore Q75I93  Go to UniProtKB:  Q75I93

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose	C, D, E	4		N/A
Glycosylation Resources
GlyTouCan:  G00025MO GlyCosmos:  G00025MO GlyGen:  G00025MO

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MES	H [auth A], J [auth B]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C6 H13 N O4 S SXGZJKUKBWWHRA-UHFFFAOYSA-N
SO4	G [auth A], I [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
ZN	F [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900011	C, D, E	beta-cellotetraose	Oligosaccharide / Metabolism

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.11 Å
• R-Value Free:  0.206 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.173 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.174 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79.433	α = 90
b = 101.508	β = 90
c = 127.317	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
REFMAC	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-02-15 
Deposition Author(s): Pengthaisong, S., Withers, S.G., Kuaprasert, B., Ketudat Cairns, J.R.

Revision History  

• Version 1.0: 2012-02-15
  Type: Initial release
  
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Structure summary
• Version 2.1: 2023-11-01
  Changes: Data collection, Database references, Refinement description, Structure summary
• Version 2.2: 2024-10-16
  Changes: Structure summary