6KQS

Crystal Structure of GH136 lacto-N-biosidase from Eubacterium ramulus - selenomethionine derivative

• PDB DOI: https://doi.org/10.2210/pdb6KQS/pdb

• Classification: HYDROLASE
• Organism(s): Eubacterium ramulus ATCC 29099
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2019-08-18 Released: 2020-06-10 
• Deposition Author(s): Yamada, C., Arakawa, T., Pichler, M.J., Abou Hachem, M., Fushinobu, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free: 0.172 
• R-Value Work: 0.149 
• R-Value Observed: 0.150 

Biological Assembly 1  

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

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

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 77.33 kDa 
• Atom Count: 5,920 
• Modelled Residue Count: 620 
• Deposited Residue Count: 665 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
lacto-N-biosidase	A	665	Eubacterium ramulus ATCC 29099	Mutation(s): 0  Gene Names: HMPREF0373_02965
UniProt
Find proteins for U2PDT9 (Eubacterium ramulus ATCC 29099) Explore U2PDT9  Go to UniProtKB:  U2PDT9

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose	B	2		N/A
Glycosylation Resources
GlyTouCan:  G00056MO GlyCosmos:  G00056MO GlyGen:  G00056MO

Small Molecules

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

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free: 0.172 
• R-Value Work: 0.149 
• R-Value Observed: 0.150 
• Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 132.734	α = 90
b = 132.734	β = 90
c = 82.466	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
XDS	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-06-10 
Deposition Author(s): Yamada, C., Arakawa, T., Pichler, M.J., Abou Hachem, M., Fushinobu, S.

Revision History  

• Version 1.0: 2020-06-10
  Type: Initial release
  
• Version 1.1: 2020-07-15
  Changes: Database references
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary