3Q10 | pdb_00003q10

Pantoate-beta-alanine ligase from Yersinia pestis

• PDB DOI: https://doi.org/10.2210/pdb3Q10/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: 1.83 Å
• R-Value Free: 
  0.211 (Depositor), 0.227 (DCC) 
• R-Value Work: 
  0.174 (Depositor), 0.188 (DCC) 
• R-Value Observed: 
  0.175 (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: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 Pseudo Symmetry: Cyclic - C2  (Explore in 3D)
Pseudo Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content 

• Total Structure Weight: 130.28 kDa 
• Atom Count: 9,440 
• Modeled Residue Count: 1,052 
• 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 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AMP	E [auth A], I [auth B], L [auth C], N [auth D]	ADENOSINE MONOPHOSPHATE C10 H14 N5 O7 P UDMBCSSLTHHNCD-KQYNXXCUSA-N
GOL	F [auth A], J [auth B], K [auth B], M [auth C], O [auth D]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
IMD	G [auth A]	IMIDAZOLE C3 H5 N2 RAXXELZNTBOGNW-UHFFFAOYSA-O
CL	H [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.83 Å
• R-Value Free:  0.211 (Depositor), 0.227 (DCC) 
• R-Value Work:  0.174 (Depositor), 0.188 (DCC) 
• R-Value Observed: 0.175 (Depositor) 

Diffraction Data: https://doi.org/10.18430/m33q10

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.809	α = 101.33
b = 77.241	β = 94.91
c = 98.462	γ = 94.37

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