2FB9

Crystal structure of the Apo form of D-alanine: D-alanine ligase (Ddl) from Thermus caldophilus: a basis for the substrate-induced conformational changes

• PDB DOI: https://doi.org/10.2210/pdb2FB9/pdb

• Classification: LIGASE
• Organism(s): Thermus caldophilus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2005-12-08 Released: 2006-08-29 
• Deposition Author(s): Lee, J.H., Na, Y., Eom, S.H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.268 
• R-Value Work: 0.228 
• R-Value Observed: 0.232 

Literature

Crystal structure of the apo form of D-alanine: D-alanine ligase (Ddl) from Thermus caldophilus: A basis for the substrate-induced conformational changes

Lee, J.H., Na, Y., Song, H.E., Kim, D., Park, B.H., Rho, S.H., Im, Y.J., Kim, M.K., Kang, G.B., Lee, D.S., Eom, S.H.

(2006) Proteins 64: 1078-1082

• PubMed: 16779845 
• DOI: https://doi.org/10.1002/prot.20927
• Primary Citation of Related Structures:  
  2FB9

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Organizational Affiliation: 

Department of Life Science, Gwangju Institute of Science & Technology, Gwangju, Korea.

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,PQS (software)

Macromolecule Content

• Total Structure Weight: 35.11 kDa 
• Atom Count: 2,596 
• Modelled Residue Count: 322 
• Deposited Residue Count: 322 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
D-alanine:D-alanine ligase	A	322	Thermus caldophilus	Mutation(s): 0  EC: 6.3.2.4
UniProt
Find proteins for Q3T920 (Thermus caldophilus) Explore Q3T920  Go to UniProtKB:  Q3T920

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.268 
• R-Value Work: 0.228 
• R-Value Observed: 0.232 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 115.216	α = 90
b = 132.744	β = 90
c = 59.324	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
SCALEPACK	data scaling
AMoRE	phasing
CNS	refinement
HKL-2000	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-08-29 
Deposition Author(s): Lee, J.H., Na, Y., Eom, S.H.

Revision History  

• Version 1.0: 2006-08-29
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance
• Version 1.3: 2024-03-13
  Changes: Data collection, Database references