3E5N | pdb_00003e5n

Crystal structure of D-alanine-D-alanine ligase from Xanthomonas oryzae pv. oryzae KACC10331

• PDB DOI: https://doi.org/10.2210/pdb3E5N/pdb

• Classification: LIGASE
• Organism(s): Xanthomonas oryzae pv. oryzae MAFF 311018
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-08-14 Released: 2009-08-18 
• Deposition Author(s): Doan, T.N.T., Kim, J.K., Kim, H.S., Ahn, Y.J., Kim, J.G., Lee, B.M., Kang, L.W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.265 (Depositor), 0.271 (DCC) 
• R-Value Work: 
  0.196 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.199 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of D-alanine-D-alanine ligase from Xanthomonas oryzae pv. oryzae KACC10331

Doan, T.N.T., Kim, J.K., Kim, H.S., Ahn, Y.J., Kim, J.G., Lee, B.M., Kang, L.W.

To be published.

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: 41.95 kDa 
• Atom Count: 2,724 
• Modeled Residue Count: 340 
• Deposited Residue Count: 386 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
D-alanine-D-alanine ligase A	A	386	Xanthomonas oryzae pv. oryzae MAFF 311018	Mutation(s): 0  Gene Names: XOO0324

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.265 (Depositor), 0.271 (DCC) 
• R-Value Work:  0.196 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.199 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 83.043	α = 90
b = 83.043	β = 90
c = 97.601	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
PHASES	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-08-18 
Deposition Author(s): Doan, T.N.T., Kim, J.K., Kim, H.S., Ahn, Y.J., Kim, J.G., Lee, B.M., Kang, L.W.

Revision History  

• Version 1.0: 2009-08-18
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2020-09-09
  Changes: Database references, Structure summary
• Version 1.3: 2023-11-01
  Changes: Data collection, Database references, Refinement description