6D5D | pdb_00006d5d

Structure of Caldicellulosiruptor danielii GH48 module of glycoside hydrolase WP_045175321

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

• Classification: HYDROLASE
• Organism(s): Anaerocellum 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 (Depositor), 0.238 (DCC) 
• R-Value Work: 
  0.163 (Depositor), 0.173 (DCC) 
• R-Value Observed: 
  0.166 (Depositor) 

Starting Model: experimental

Literature

Novel multidomain, multifunctional glycoside hydrolases from highly lignocellulolytic Caldicellulosiruptor species

Conway, J.M., Crosby, J.R., Hren, A.P., Southerland, R.T., Lee, L.L., Lunin, V.V., Alahuhta, P.M., Himmel, M.E., Bomble, Y.J., Adams, M.W.W., Kelly, R.M.

(2019) AIChE J 

• DOI: https://doi.org/10.1002/aic.16354

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 
• Modeled 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	Anaerocellum danielii	Mutation(s): 0  EC: 3.2.1
UniProt
Find proteins for A0A4V8GZQ9 (Anaerocellum danielii) Explore A0A4V8GZQ9  Go to UniProtKB:  A0A4V8GZQ9

Oligosaccharides

Help  

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D 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 (Depositor), 0.238 (DCC) 
• R-Value Work:  0.163 (Depositor), 0.173 (DCC) 
• R-Value Observed: 0.166 (Depositor) 

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