3Q12 | pdb_00003q12

Pantoate-beta-alanine ligase from Yersinia pestis in complex with pantoate.

• PDB DOI: https://doi.org/10.2210/pdb3Q12/pdb

• Classification: LIGASE
• Organism(s): Yersinia pestis
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2010-12-16 Released: 2011-02-02 
• Deposition Author(s): Osipiuk, J., Maltseva, N., Kwon, K., 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: 1.58 Å
• R-Value Free: 
  0.195 (Depositor), 0.197 (DCC) 
• R-Value Work: 
  0.150 (Depositor), 0.153 (DCC) 
• R-Value Observed: 
  0.152 (Depositor) 

Starting Model: experimental

Literature

Pantoate-beta-alanine ligase from Yersinia pestis.

Osipiuk, J., Maltseva, N., Kwon, K., 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)

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 128.98 kDa 
• Atom Count: 10,600 
• Modeled Residue Count: 1,137 
• Deposited Residue Count: 1,148 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Pantoate--beta-alanine ligase	A, B, C, D	287	Yersinia pestis	Mutation(s): 0  Gene Names: panC, y0785, YPO3402, YP_0283 EC: 6.3.2.1
UniProt
Find proteins for Q8ZBK7 (Yersinia pestis) Explore Q8ZBK7  Go to UniProtKB:  Q8ZBK7

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PAF	E [auth A], G [auth B], H [auth C], J [auth D]	PANTOATE C6 H11 O4 OTOIIPJYVQJATP-BYPYZUCNSA-M
CL	F [auth A], I [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.58 Å
• R-Value Free:  0.195 (Depositor), 0.197 (DCC) 
• R-Value Work:  0.150 (Depositor), 0.153 (DCC) 
• R-Value Observed: 0.152 (Depositor) 

Diffraction Data: https://doi.org/10.18430/m33q12

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.73	α = 100.67
b = 77.054	β = 95.33
c = 98.757	γ = 94.43

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: 2011-02-02 
Deposition Author(s): Osipiuk, J., Maltseva, N., Kwon, K., Anderson, W.F., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History  

• Version 1.0: 2011-02-02
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-11-08
  Changes: Refinement description
• Version 1.3: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description