3INN | pdb_00003inn

Crystal structure of pantoate-beta-alanine-ligase in complex with ATP at low occupancy at 2.1 A resolution

• PDB DOI: https://doi.org/10.2210/pdb3INN/pdb

• Classification: LIGASE
• Organism(s): Brucella melitensis
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-08-12 Released: 2009-10-06 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.245 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.194 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.196 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of pantoate-beta-alanine-ligase in complex with ATP at low occupancy at 2.1 A resolution

Seattle Structural Genomics Center for Infectious Disease (SSGCID), Abendroth, J., Davies, D., Staker, B.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 140.86 kDa 
• Atom Count: 9,322 
• Modeled Residue Count: 1,122 
• Deposited Residue Count: 1,256 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Pantothenate synthetase	A, B, C, D	314	Brucella melitensis	Mutation(s): 0  Gene Names: BMEI1593, panC EC: 6.3.2.1
UniProt
Find proteins for Q8YFC9 (Brucella melitensis biotype 1 (strain ATCC 23456 / CCUG 17765 / NCTC 10094 / 16M)) Explore Q8YFC9  Go to UniProtKB:  Q8YFC9

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ATP	E [auth A], I [auth C], M [auth D]	ADENOSINE-5'-TRIPHOSPHATE C10 H16 N5 O13 P3 ZKHQWZAMYRWXGA-KQYNXXCUSA-N
UNX	F [auth A], G [auth A], H [auth A], J [auth C], K [auth C], L [auth C]	UNKNOWN ATOM OR ION X

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.245 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.194 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.196 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M33INN

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 94.32	α = 90
b = 94.32	β = 90
c = 236.93	γ = 120

Software Package:

Software Name	Purpose
Blu-Ice	data collection
PHASER	phasing
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-10-06 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History  

• Version 1.0: 2009-10-06
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-09-06
  Changes: Data collection, Database references, Derived calculations, Refinement description