4Q22

Crystal structure of Chitinase D from Serratia proteamaculans in complex with N-acetyl glucosamine at 1.93 Angstrom resolution

• PDB DOI: https://doi.org/10.2210/pdb4Q22/pdb

• Classification: HYDROLASE
• Organism(s): Serratia proteamaculans 568
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2014-04-05 Released: 2014-04-23 
• Deposition Author(s): Kushwaha, G.S., Madhuprakash, J., Singh, A., Bhushan, A., Sinha, M., Kaur, P., Sharma, S., Podile, A.R., Singh, T.P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.93 Å
• R-Value Free: 0.196 
• R-Value Work: 0.162 
• R-Value Observed: 0.164 

Literature

Crystal structure of Chitinase D from Serratia proteamaculans in complex with N-acetyl glucosamine at 1.93 Angstrom resolution

Kushwaha, G.S., Madhuprakash, J., Singh, A., Bhushan, A., Sinha, M., Kaur, P., Sharma, S., Podile, A.R., Singh, T.P.

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)

Macromolecule Content

• Total Structure Weight: 44.49 kDa 
• Atom Count: 3,598 
• Modelled Residue Count: 398 
• Deposited Residue Count: 398 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycoside hydrolase family 18	A	398	Serratia proteamaculans 568	Mutation(s): 0  Gene Names: Spro_2725 EC: 3.2.1.14
UniProt
Find proteins for A8GFD6 (Serratia proteamaculans (strain 568)) Explore A8GFD6  Go to UniProtKB:  A8GFD6

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	B [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
GOL	D [auth A], E [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ACT	C [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
OMT	A	L-PEPTIDE LINKING	C5 H11 N O4 S		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.93 Å
• R-Value Free: 0.196 
• R-Value Work: 0.162 
• R-Value Observed: 0.164 
• Space Group: P 2 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.211	α = 90
b = 74.918	β = 90
c = 87.049	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
MOLREP	phasing
REFMAC	refinement
AUTOMAR	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-04-23 
Deposition Author(s): Kushwaha, G.S., Madhuprakash, J., Singh, A., Bhushan, A., Sinha, M., Kaur, P., Sharma, S., Podile, A.R., Singh, T.P.

Revision History  

• Version 1.0: 2014-04-23
  Type: Initial release
  
• Version 1.1: 2015-04-01
  Changes: Experimental preparation
• Version 1.2: 2016-04-20
  Changes: Experimental preparation
• Version 1.3: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary
• Version 1.4: 2023-11-08
  Changes: Data collection, Database references, Refinement description, Structure summary