Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

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

Macromolecule Content

• Total Structure Weight: 27.77 kDa 
• Atom Count: 2216 
• Modelled Residue Count: 225 
• Deposited Residue Count: 244 
• Unique protein chains: 1

1NQD

CRYSTAL STRUCTURE OF CLOSTRIDIUM HISTOLYTICUM COLG COLLAGENASE COLLAGEN-BINDING DOMAIN 3B AT 1.65 ANGSTROM RESOLUTION IN PRESENCE OF CALCIUM

• DOI: 10.2210/pdb1NQD/pdb

• Classification: HYDROLASE
• Organism(s): Hathewaya histolytica
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2003-01-21 Released: 2003-04-15 
• Deposition Author(s): Wilson, J.J., Matsushita, O., Okabe, A., Sakon, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 0.254 
• R-Value Work: 0.185 
• R-Value Observed: 0.191 

Literature

A Bacterial Collagen-Binding Domain with Novel Calcium-Binding Motif Controls Domain Orientation

Wilson, J.J., Matsushita, O., Okabe, A., Sakon, J.

(2003) EMBO J 22: 1743-1752

• PubMed: 12682007 
• DOI: 10.1093/emboj/cdg172
• Primary Citation of Related Structures:  
  1NQJ, 1NQD


• PubMed Abstract: 
  

The crystal structure of a collagen-binding domain (CBD) with an N-terminal domain linker from Clostridium histolyticum class I collagenase was determined at 1.00 A resolution in the absence of calcium (1NQJ) and at 1.65 A resolution in the presence of calcium (1NQD). The mature enzyme is composed of four domains: a metalloprotease domain, a spacing domain and two CBDs. A 12-residue-long linker is found at the N-terminus of each CBD. In the absence of calcium, the CBD reveals a beta-sheet sandwich fold with the linker adopting an alpha-helix. The addition of calcium unwinds the linker and anchors it to the distal side of the sandwich as a new beta-strand. The conformational change of the linker upon calcium binding is confirmed by changes in the Stokes and hydrodynamic radii as measured by size exclusion chromatography and by dynamic light scattering with and without calcium. Furthermore, extensive mutagenesis of conserved surface residues and collagen-binding studies allow us to identify the collagen-binding surface of the protein and propose likely collagen-protein binding models.

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Organizational Affiliation: 

Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR 72701, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
class 1 collagenase	A, B	122	Hathewaya histolytica	Mutation(s): 0  Gene Names: colG EC: 3.4.24.3
Find proteins for Q9X721 (Hathewaya histolytica) Explore Q9X721  Go to UniProtKB:  Q9X721

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA	A, B	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 0.254 
• R-Value Work: 0.185 
• R-Value Observed: 0.191 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 40.867	α = 90
b = 59.401	β = 98.73
c = 48.572	γ = 90

Software Package:

Software Name	Purpose
SHELXL-97	refinement
HKL-2000	data reduction
CNS	refinement
SHELX	model building
HKL-2000	data collection
HKL-2000	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2003-01-21 
• Released Date: 2003-04-15 
Deposition Author(s): Wilson, J.J., Matsushita, O., Okabe, A., Sakon, J.

Revision History  

• Version 1.0: 2003-04-15
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2019-07-24
  Changes: Data collection, Refinement description