4JCW | pdb_00004jcw

Crystal structure of Clavibacter michiganensis expansin in complex with cellopentaose

• PDB DOI: https://doi.org/10.2210/pdb4JCW/pdb

• Classification: SUGAR BINDING PROTEIN
• Organism(s): Clavibacter michiganensis subsp. michiganensis NCPPB 382
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2013-02-22 Released: 2014-03-05 
• Deposition Author(s): Yennawar, N.H., Yennawar, H.P., Georgelis, N., Cosgrove, D.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 
  0.225 (Depositor), 0.244 (DCC) 
• R-Value Work: 
  0.173 (Depositor) 
• R-Value Observed: 
  0.176 (Depositor) 

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.J.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 44.41 kDa 
• Atom Count: 3,624 
• Modeled 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	202	Clavibacter michiganensis subsp. michiganensis NCPPB 382	Mutation(s): 0  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	D Interactions
beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose	C	5		N/A
Glycosylation Resources
GlyTouCan: G91683DU GlyCosmos: G91683DU

Biologically Interesting Molecules (External Reference) 

1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900016	C	beta-cellopentaose	Oligosaccharide / Metabolism

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free:  0.225 (Depositor), 0.244 (DCC) 
• R-Value Work:  0.173 (Depositor) 
• R-Value Observed: 0.176 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 35.936	α = 88.75
b = 43.212	β = 81.29
c = 64.3	γ = 82.7

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: 2014-03-05 
Deposition Author(s): Yennawar, N.H., Yennawar, H.P., Georgelis, N., Cosgrove, D.J.

Revision History  

• Version 1.0: 2014-03-05
  Type: Initial release
  
• Version 1.1: 2015-06-24
  Changes: Derived calculations
• 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