2ZDQ | pdb_00002zdq

Crystal structure of D-Alanine:D-Alanine Ligase with ATP and D-Alanine:D-Alanine from Thermus thermophius HB8

• PDB DOI: https://doi.org/10.2210/pdb2ZDQ/pdb

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


• Deposited: 2007-11-27 Released: 2008-05-27 
• Deposition Author(s): Kitamuta, Y., Yokoyama, S., Kuramitsu, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.266 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.231 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.231 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of D-Alanine:D-Alanine Ligase with ATP and D-Alanine:D-Alanine from Thermus thermophius HB8

Kitamura, Y., Yokoyama, S., Kuramitsu, S.

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: 70.77 kDa 
• Atom Count: 5,184 
• Modeled Residue Count: 638 
• Deposited Residue Count: 638 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
D-alanine--D-alanine ligase	A, B	319	Thermus thermophilus	Mutation(s): 0  EC: 6.3.2.4
UniProt
Find proteins for Q5SHZ3 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SHZ3  Go to UniProtKB:  Q5SHZ3

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ATP	E [auth A], H [auth B]	ADENOSINE-5'-TRIPHOSPHATE C10 H16 N5 O13 P3 ZKHQWZAMYRWXGA-KQYNXXCUSA-N
DAL	C [auth A], D [auth A], F [auth B], G [auth B]	D-ALANINE C3 H7 N O2 QNAYBMKLOCPYGJ-UWTATZPHSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.266 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.231 (Depositor), 0.220 (DCC) 
• R-Value Observed: 0.231 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 95.052	α = 90
b = 95.052	β = 90
c = 192.009	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
BSS	data collection
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-05-27 
Deposition Author(s): Kitamuta, Y., Yokoyama, S., Kuramitsu, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History  

• Version 1.0: 2008-05-27
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description