Biological Assembly 1  

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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: 27770.69 
• Atom Count: 1903 
• 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


• 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 

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


• 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

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
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) Go to UniProtKB:  Q9X721

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
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 
• Space Group: P 1 2₁ 1

Unit Cell:

Length (Å)	Angle (°)
a = 40.867	α = 90.00
b = 59.401	β = 98.73
c = 48.572	γ = 90.00

Software Package:

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

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
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Version format compliance