5M6G | pdb_00005m6g

Crystal structure Glucan 1,4-beta-glucosidase from Saccharopolyspora erythraea

• PDB DOI: https://doi.org/10.2210/pdb5M6G/pdb

• Classification: HYDROLASE
• Organism(s): Saccharopolyspora erythraea D
• Expression System: Komagataella phaffii GS115
• Mutation(s): No 


• Deposited: 2016-10-25 Released: 2017-11-29 
• Deposition Author(s): Gabdulkhakov, A., Tishchenko, S., Lisov, A., Leontievsky, A.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.83 Å
• R-Value Free: 
  0.203 (Depositor), 0.206 (DCC) 
• R-Value Work: 
  0.172 (Depositor), 0.174 (DCC) 
• R-Value Observed: 
  0.173 (Depositor) 

Starting Model: experimental

Literature

Crystal structure Glucan 1,4-beta-glucosidase from Saccharopolyspora erythraea

Gabdulkhakov, A., Tishchenko, S.

To be published.

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 66.13 kDa 
• Atom Count: 4,695 
• Modeled Residue Count: 579 
• Deposited Residue Count: 615 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-glucosidase	A	615	Saccharopolyspora erythraea D	Mutation(s): 0  Gene Names: celD, SACE_6502, A8924_6851 EC: 3.2.1.74 (PDB Primary Data), 3.2.1.21 (UniProt)
UniProt
Find proteins for A4FNP6 (Saccharopolyspora erythraea (strain ATCC 11635 / DSM 40517 / JCM 4748 / NBRC 13426 / NCIMB 8594 / NRRL 2338)) Explore A4FNP6  Go to UniProtKB:  A4FNP6

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SOR	L [auth A]	sorbitol C6 H14 O6 FBPFZTCFMRRESA-JGWLITMVSA-N
PGE	K [auth A]	TRIETHYLENE GLYCOL C6 H14 O4 ZIBGPFATKBEMQZ-UHFFFAOYSA-N
GOL	H [auth A], I [auth A], J [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
MG	B [auth A], C [auth A], D [auth A], 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: 1.83 Å
• R-Value Free:  0.203 (Depositor), 0.206 (DCC) 
• R-Value Work:  0.172 (Depositor), 0.174 (DCC) 
• R-Value Observed: 0.173 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.292	α = 90
b = 75.717	β = 90
c = 113.893	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-11-29 
Deposition Author(s): Gabdulkhakov, A., Tishchenko, S., Lisov, A., Leontievsky, A.

Revision History  

• Version 1.0: 2017-11-29
  Type: Initial release
  
• Version 1.1: 2019-10-16
  Changes: Data collection, Database references, Source and taxonomy, Structure summary
• Version 1.2: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Derived calculations, Structure summary
• Version 1.3: 2024-01-17
  Changes: Data collection, Database references, Refinement description, Structure summary
• Version 1.4: 2024-10-23
  Changes: Structure summary