2CIT | pdb_00002cit

Structure of the covalent intermediate of a family 26 lichenase

• PDB DOI: https://doi.org/10.2210/pdb2CIT/pdb

• Classification: HYDROLASE
• Organism(s): Acetivibrio thermocellus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2006-03-24 Released: 2006-04-10 
• Deposition Author(s): Money, V.A., Smith, N.L., Scaffidi, A., Stick, R.V., Gilbert, H.J., Davies, G.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free: 
  0.179 (Depositor), 0.178 (DCC) 
• R-Value Work: 
  0.151 (Depositor), 0.149 (DCC) 
• R-Value Observed: 
  0.152 (Depositor) 

Literature

Substrate Distortion by a Lichenase Highlights the Different Conformational Itineraries Harnessed by Related Glycoside Hydrolases.

Money, V.A., Smith, N.L., Scaffidi, A., Stick, R.V., Gilbert, H.J., Davies, G.J.

(2006) Angew Chem Int Ed Engl 45: 5136

• PubMed: 16823793 
• DOI: https://doi.org/10.1002/anie.200600802
• Primary Citation Related Structures: 
  2CIP, 2CIT

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Organizational Affiliation: 
• York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5YW, UK.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 32.57 kDa 
• Atom Count: 2,802 
• Modeled Residue Count: 274 
• Deposited Residue Count: 282 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ENDOGLUCANASE H	A	282	Acetivibrio thermocellus	Mutation(s): 1  EC: 3.2.1.4
UniProt
Find proteins for P16218 (Acetivibrio thermocellus (strain ATCC 27405 / DSM 1237 / JCM 9322 / NBRC 103400 / NCIMB 10682 / NRRL B-4536 / VPI 7372)) Explore P16218  Go to UniProtKB:  P16218
Glycosylation
Glycosylation Sites: 1

Oligosaccharides

Help  

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-3)-2-deoxy-2-fluoro-alpha-D-glucopyranose	B	3		N/A
Glycosylation Resources
GlyTouCan: G57974FK GlyCosmos: G57974FK

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free:  0.179 (Depositor), 0.178 (DCC) 
• R-Value Work:  0.151 (Depositor), 0.149 (DCC) 
• R-Value Observed: 0.152 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.047	α = 90
b = 62.83	β = 90
c = 78.057	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-04-10 
Deposition Author(s): Money, V.A., Smith, N.L., Scaffidi, A., Stick, R.V., Gilbert, H.J., Davies, G.J.

Revision History  

• Version 1.0: 2006-04-10
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Other, Structure summary
• Version 2.1: 2024-10-16
  Changes: Data collection, Database references, Structure summary