4WIW | pdb_00004wiw

Crystal structure of C-terminal domain of putative chitinase from Desulfitobacterium hafniense DCB-2

• PDB DOI: https://doi.org/10.2210/pdb4WIW/pdb

• Classification: HYDROLASE
• Organism(s): Desulfitobacterium hafniense DCB-2
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2014-09-26 Released: 2014-10-08 
• Deposition Author(s): Chang, C., Tesar, C., Endres, M., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.64 Å
• R-Value Free: 
  0.236 (Depositor), 0.238 (DCC) 
• R-Value Work: 
  0.184 (Depositor), 0.192 (DCC) 
• R-Value Observed: 
  0.187 (Depositor) 

Literature

Crystal structure of C-terminal domain of putative chitinase from Desulfitobacterium hafniense DCB-2

Chang, C., Tesar, C., Endres, M., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

To be published.

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Biological Assembly 2  

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

Biological assembly 2 generated by PISA (software)

Biological Assembly 3  

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

Biological assembly 3 generated by PISA (software)

Biological Assembly 4  

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

Biological assembly 4 generated by PISA (software)

Biological Assembly 5  

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

Biological assembly 5 generated by PISA (software)

Biological Assembly 6  

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

Biological assembly 6 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 237.1 kDa 
• Atom Count: 16,700 
• Modeled Residue Count: 2,089 
• Deposited Residue Count: 2,094 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycoside hydrolase family 18	A, B, C, D, E, F	349	Desulfitobacterium hafniense DCB-2	Mutation(s): 0  Gene Names: Dhaf_4489
UniProt
Find proteins for B8FWJ2 (Desulfitobacterium hafniense (strain DSM 10664 / DCB-2)) Explore B8FWJ2  Go to UniProtKB:  B8FWJ2

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PEG	P [auth D]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
CA	G [auth A], H [auth A], I [auth A], J [auth A], L [auth B], M [auth C], N [auth D], O [auth D], Q [auth E], R [auth F]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL	K [auth A], S [auth F]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B, C, D, E, F	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.64 Å
• R-Value Free:  0.236 (Depositor), 0.238 (DCC) 
• R-Value Work:  0.184 (Depositor), 0.192 (DCC) 
• R-Value Observed: 0.187 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79.933	α = 90
b = 346.625	β = 90
c = 193.442	γ = 90

Software Package:

Software Name	Purpose
HKL-3000	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
SCALEPACK	data scaling
SBC-Collect	data collection

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-10-08 
Deposition Author(s): Chang, C., Tesar, C., Endres, M., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2014-10-08
  Type: Initial release
  
• Version 1.1: 2015-02-04
  Changes: Derived calculations
• Version 1.2: 2017-11-22
  Changes: Derived calculations, Other, Refinement description, Source and taxonomy
• Version 1.3: 2023-12-27
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.4: 2024-10-16
  Changes: Structure summary