3V4Z | pdb_00003v4z

D-alanine--D-alanine ligase from Yersinia pestis

• PDB DOI: https://doi.org/10.2210/pdb3V4Z/pdb

• Classification: LIGASE
• Organism(s): Yersinia pestis CO92
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2011-12-15 Released: 2011-12-28 
• Deposition Author(s): Osipiuk, J., Nocek, B., Mulligan, R., Papazisi, L., Anderson, W.F., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.69 Å
• R-Value Free: 
  0.289 (Depositor), 0.280 (DCC) 
• R-Value Work: 
  0.205 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.209 (Depositor) 

Starting Model: experimental

Literature

D-alanine--D-alanine ligase from Yersinia pestis.

Osipiuk, J., Nocek, B., Mulligan, R., Papazisi, L., Anderson, W.F., Joachimiak, A.

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: 67.16 kDa 
• Atom Count: 4,439 
• Modeled Residue Count: 580 
• Deposited Residue Count: 618 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
D-alanine--D-alanine ligase	A, B	309	Yersinia pestis CO92	Mutation(s): 0  Gene Names: ddl, ddlB, y3624, YPO0557, YP_3627 EC: 6.3.2.4
UniProt
Find proteins for Q8ZIE7 (Yersinia pestis) Explore Q8ZIE7  Go to UniProtKB:  Q8ZIE7

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PGE	D [auth B]	TRIETHYLENE GLYCOL C6 H14 O4 ZIBGPFATKBEMQZ-UHFFFAOYSA-N
PEG	C [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.69 Å
• R-Value Free:  0.289 (Depositor), 0.280 (DCC) 
• R-Value Work:  0.205 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.209 (Depositor) 

Diffraction Data: https://doi.org/10.18430/m33v4z

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 100.637	α = 90
b = 100.637	β = 90
c = 110.304	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
SBC-Collect	data collection
HKL-3000	data reduction
HKL-3000	data scaling
MOLREP	phasing
HKL-3000	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-12-28 
Deposition Author(s): Osipiuk, J., Nocek, B., Mulligan, R., Papazisi, L., Anderson, W.F., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History  

• Version 1.0: 2011-12-28
  Type: Initial release
  
• Version 1.1: 2017-11-08
  Changes: Refinement description
• Version 1.2: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description