6D5D

Structure of Caldicellulosiruptor danielii GH48 module of glycoside hydrolase WP_045175321

• PDB DOI: https://doi.org/10.2210/pdb6D5D/pdb

• Classification: HYDROLASE
• Organism(s): Caldicellulosiruptor danielii
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2018-04-19 Released: 2019-04-24 
• Deposition Author(s): Alahuhta, P.M., Lunin, V.V.
• Funding Organization(s): Department of Energy (DOE, United States)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.231 
• R-Value Work: 0.163 
• R-Value Observed: 0.166 

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: 74.52 kDa 
• Atom Count: 6,063 
• Modelled Residue Count: 627 
• Deposited Residue Count: 645 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
glycoside hydrolase WP_045175321	A	645	Caldicellulosiruptor danielii	Mutation(s): 0  EC: 3.2.1
UniProt
Find proteins for A0A4V8GZQ9 (Caldicellulosiruptor danielii) Explore A0A4V8GZQ9  Go to UniProtKB:  A0A4V8GZQ9

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-glucopyranose-(1-4)-beta-D-glucopyranose	B, C	2		N/A
Glycosylation Resources
GlyTouCan:  G84824ZO GlyCosmos:  G84824ZO

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA	D [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900005	B, C	beta-cellobiose	Oligosaccharide / Metabolism

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.231 
• R-Value Work: 0.163 
• R-Value Observed: 0.166 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 116.014	α = 90
b = 57.512	β = 103.38
c = 105.957	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
SAINT	data reduction
PROTEUM PLUS	data scaling
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2019-04-24 
Deposition Author(s): Alahuhta, P.M., Lunin, V.V.

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Funding Organization	Location	Grant Number
Department of Energy (DOE, United States)	United States	--

Revision History  

• Version 1.0: 2019-04-24
  Type: Initial release
  
• Version 1.1: 2019-06-05
  Changes: Data collection, Database references
• Version 1.2: 2019-12-04
  Changes: Author supporting evidence
• 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: 2023-10-04
  Changes: Data collection, Database references, Refinement description, Structure summary