3JUL | pdb_00003jul

Crystal structure of Listeria innocua D-Tagatose-6-Phosphate Kinase bound with substrate

• PDB DOI: https://doi.org/10.2210/pdb3JUL/pdb

• Classification: TRANSFERASE
• Organism(s): Listeria innocua
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2009-09-15 Released: 2009-10-06 
• Deposition Author(s): Satyanarayana, L., Burley, S.K., Swaminathan, S., New York SGX Research Center for Structural Genomics (NYSGXRC)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 
  0.267 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.226 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.226 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of Listeria innocua D-Tagatose-6-Phosphate Kinase bound with substrate

Satyanarayana, L., Burley, S.K., Swaminathan, 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: 35.62 kDa 
• Atom Count: 2,362 
• Modeled Residue Count: 298 
• Deposited Residue Count: 320 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lin2199 protein	A	320	Listeria innocua	Mutation(s): 0  Gene Names: lin2199 EC: 2.7.1.144
UniProt
Find proteins for Q929S5 (Listeria innocua serovar 6a (strain ATCC BAA-680 / CLIP 11262)) Explore Q929S5  Go to UniProtKB:  Q929S5

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TA6	C [auth A]	6-O-phosphono-beta-D-tagatofuranose C6 H13 O9 P BGWGXPAPYGQALX-DPYQTVNSSA-N
MG	B [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free:  0.267 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.226 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.226 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 84.307	α = 90
b = 44.24	β = 104.65
c = 79.116	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-10-06 
Deposition Author(s): Satyanarayana, L., Burley, S.K., Swaminathan, S., New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History  

• Version 1.0: 2009-10-06
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Database references, Derived calculations, Structure summary
• Version 2.1: 2021-02-10
  Changes: Database references, Structure summary
• Version 2.2: 2023-09-06
  Changes: Data collection, Database references, Refinement description
• Version 2.3: 2023-11-22
  Changes: Data collection
• Version 2.4: 2024-11-06
  Changes: Structure summary