1GOI | pdb_00001goi

Crystal structure of the D140N mutant of chitinase B from Serratia marcescens at 1.45 A resolution

• PDB DOI: https://doi.org/10.2210/pdb1GOI/pdb

• Classification: HYDROLASE
• Organism(s): Serratia marcescens
• Mutation(s): Yes 


• Deposited: 2001-10-21 Released: 2001-11-15 
• Deposition Author(s): Kolstad, G., Synstad, B., Eijsink, V.G.H., Van Aalten, D.M.F.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free: 
  0.220 (Depositor), 0.204 (DCC) 
• R-Value Work: 
  0.157 (DCC) 
• R-Value Observed: 
  0.160 (Depositor) 

Starting Model: experimental

Literature

Structure of the D140N Mutant of Chitinase B from Serratia Marcescens at 1.45 A Resolution.

Kolstad, G., Synstad, B., Eijsink, V.G.H., Van Aalten, D.M.F.

(2002) Acta Crystallogr D Biol Crystallogr 58: 377

• PubMed: 11807282 
• DOI: https://doi.org/10.1107/s0907444901018972
• Primary Citation Related Structures: 
  1GOI


• PubMed Abstract: 
  

  The crystal structure of the inactive D140N mutant of Serratia marcescens was refined to 1.45 A resolution. The structure of the mutant was essentially identical to that of the wild type, with the exception of a rotation of Asp142 in the catalytic centre. In the mutant, this residue interacts with the catalytic acid (Glu144) and not with residue 140 as in the wild type. Thus, the 500-fold decrease in activity in the D140N mutant seems to be largely mediated by an effect on Asp142, confirming the crucial role of the latter residue in catalysis.

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Organizational Affiliation: 
• Department of Chemistry and Biotechnology, Agricultural University of Norway, 1432 As, Norway.

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 112.52 kDa 
• Atom Count: 8,990 
• Modeled Residue Count: 994 
• Deposited Residue Count: 998 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CHITINASE B	A, B	499	Serratia marcescens	Mutation(s): 1  EC: 3.2.1.14
UniProt
Find proteins for P11797 (Serratia marcescens) Explore P11797  Go to UniProtKB:  P11797

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	I [auth A], P [auth B], Q [auth B], R [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], J [auth B], K [auth B], L [auth B], M [auth B], N [auth B], O [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free:  0.220 (Depositor), 0.204 (DCC) 
• R-Value Work:  0.157 (DCC) 
• R-Value Observed: 0.160 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.904	α = 90
b = 104.016	β = 90
c = 186.524	γ = 90

Software Package:

Software Name	Purpose
SHELXL-97	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2001-11-15 
Deposition Author(s): Kolstad, G., Synstad, B., Eijsink, V.G.H., Van Aalten, D.M.F.

Revision History  

• Version 1.0: 2001-11-15
  Type: Initial release
  
• Version 1.1: 2011-09-14
  Changes: Atomic model, Database references, Derived calculations, Non-polymer description, Other, Structure summary, Version format compliance
• Version 1.2: 2023-12-13
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description
• Version 1.3: 2024-10-23
  Changes: Structure summary