6RY5

Crystal structure of Dfg5 from Chaetomium thermophilum in complex with alpha-1,6-mannobiose

• PDB DOI: https://doi.org/10.2210/pdb6RY5/pdb

• Classification: HYDROLASE
• Organism(s): Thermochaetoides thermophila DSM 1495
• Expression System: Escherichia coli B
• Mutation(s): No 
• Membrane Protein: Yes  mpstruc


• Deposited: 2019-06-10 Released: 2020-08-12 
• Deposition Author(s): Essen, L.-O., Vogt, M.S.
• Funding Organization(s): German Research Foundation

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.30 Å
• R-Value Free: 0.123 
• R-Value Work: 0.102 
• R-Value Observed: 0.103 

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: 50.12 kDa 
• Atom Count: 3,811 
• Modelled Residue Count: 410 
• Deposited Residue Count: 443 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mannan endo-1,6-alpha-mannosidase	A	443	Thermochaetoides thermophila DSM 1495	Mutation(s): 0  Gene Names: CTHT_0020800 EC: 3.2.1.101 Membrane Entity: Yes
UniProt
Find proteins for G0S3F2 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)) Explore G0S3F2  Go to UniProtKB:  G0S3F2

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose	B	2		N/A
Glycosylation Resources
GlyTouCan:  G71124KE GlyCosmos:  G71124KE GlyGen:  G71124KE

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PGE	E [auth A]	TRIETHYLENE GLYCOL C6 H14 O4 ZIBGPFATKBEMQZ-UHFFFAOYSA-N
CA	C [auth A], D [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.30 Å
• R-Value Free: 0.123 
• R-Value Work: 0.102 
• R-Value Observed: 0.103 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 83.415	α = 90
b = 55.019	β = 90.37
c = 80.119	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-08-12 
Deposition Author(s): Essen, L.-O., Vogt, M.S.

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Funding Organization	Location	Grant Number
German Research Foundation	Germany	SFB987

Revision History  

• Version 1.0: 2020-08-12
  Type: Initial release
  
• Version 1.1: 2020-08-26
  Changes: Database references
• Version 1.2: 2020-09-16
  Changes: Database references