6VC5 | pdb_00006vc5

1.6 Angstrom Resolution Crystal Structure of endoglucanase from Komagataeibacter sucrofermentans

• PDB DOI: https://doi.org/10.2210/pdb6VC5/pdb

• Classification: HYDROLASE
• Organism(s): Komagataeibacter sucrofermentans
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2019-12-20 Released: 2020-12-23 
• Deposition Author(s): Wu, R., Kim, Y., Jedrzrjczak, R., Joachimiak, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 
  0.176 (Depositor) 
• R-Value Work: 
  0.155 (Depositor) 
• R-Value Observed: 
  0.156 (Depositor) 

Starting Model: experimental

Literature

1.6 Angstrom Resolution Crystal Structure of endoglucanase from Komagataeibacter sucrofermentans

Wu, R., Kim, Y., Jedrzejczak, R., Joachimiak, A.

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)

Macromolecule Content 

• Total Structure Weight: 35.9 kDa 
• Atom Count: 2,939 
• Modeled Residue Count: 318 
• Deposited Residue Count: 321 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Endoglucanase	A	321	Komagataeibacter sucrofermentans	Mutation(s): 0  Gene Names: CMCase EC: 3.2.1.4
UniProt
Find proteins for O82857 (Komagataeibacter sucrofermentans) Explore O82857  Go to UniProtKB:  O82857

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	B [auth A], C [auth A], D [auth A], E [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free:  0.176 (Depositor) 
• R-Value Work:  0.155 (Depositor) 
• R-Value Observed: 0.156 (Depositor) 

Space Group: I 4

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 120.52	α = 90
b = 120.52	β = 90
c = 47.588	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
SCALEPACK	data scaling
PDB_EXTRACT	data extraction
HKL-3000	data reduction
HKL-3000	phasing

Structure Validation

Currently 6VC5 does not have a validation slider image.

Entry History 

Deposition Data

• Released Date: 2020-12-23 
Deposition Author(s): Wu, R., Kim, Y., Jedrzrjczak, R., Joachimiak, A.

Revision History  

• Version 1.0: 2020-12-23
  Type: Initial release
  
• Version 1.1: 2023-10-11
  Changes: Data collection, Database references, Refinement description