4L48

Crystal structure of d78n mutant clavibacter michiganensis expansin in complex with cellohexaose

• PDB DOI: https://doi.org/10.2210/pdb4L48/pdb

• Classification: SUGAR BINDING PROTEIN
• Organism(s): Clavibacter michiganensis subsp. michiganensis NCPPB 382
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2013-06-07 Released: 2014-03-26 
• Deposition Author(s): Yennawar, N.H., Yennawar, H.P., Georgelis, N., Cosgrove, D.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.257 
• R-Value Work: 0.195 
• R-Value Observed: 0.201 

Starting Model: experimental

Literature

Crystal structure of wild type and d78n mutant clavibacter michiganensis expansin, in apo form and in complex with oligosaccharides

Yennawar, N.H., Yennawar, H.P., Georgelis, N., Cosgrove, D.

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)

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 45.56 kDa 
• Atom Count: 3,862 
• Modelled Residue Count: 404 
• Deposited Residue Count: 404 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
cellulose binding protein	A, B [auth C]	202	Clavibacter michiganensis subsp. michiganensis NCPPB 382	Mutation(s): 1  Gene Names: celA, pCM1_0020 EC: 3.2.1.4
UniProt
Find proteins for A5CLK3 (Clavibacter michiganensis subsp. michiganensis (strain NCPPB 382)) Explore A5CLK3  Go to UniProtKB:  A5CLK3

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose	C [auth B], D	6		N/A
Glycosylation Resources
GlyTouCan:  G09454VW GlyCosmos:  G09454VW GlyGen:  G09454VW

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900020	C [auth B], D	beta-cellohexaose	Oligosaccharide / Metabolism

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.257 
• R-Value Work: 0.195 
• R-Value Observed: 0.201 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.758	α = 90
b = 34.555	β = 95.57
c = 81.144	γ = 90

Software Package:

Software Name	Purpose
CrystalClear	data collection
PHENIX	model building
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-03-26 
Deposition Author(s): Yennawar, N.H., Yennawar, H.P., Georgelis, N., Cosgrove, D.

Revision History  

• Version 1.0: 2014-03-26
  Type: Initial release
  
• Version 1.1: 2015-06-24
  Changes: Structure summary
• Version 1.2: 2015-10-21
  Changes: Structure summary
• 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: 2023-09-20
  Changes: Data collection, Database references, Refinement description, Structure summary
• Version 2.2: 2024-11-06
  Changes: Structure summary