4HTL | pdb_00004htl

Lmo2764 protein, a putative N-acetylmannosamine kinase, from Listeria monocytogenes

• PDB DOI: https://doi.org/10.2210/pdb4HTL/pdb

• Classification: TRANSFERASE
• Organism(s): Listeria monocytogenes EGD-e
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2012-11-01 Released: 2012-11-14 
• Deposition Author(s): Osipiuk, J., Mack, J., Endres, M., Salazar, J., Zhang, W., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.64 Å
• R-Value Free: 
  0.169 (Depositor), 0.171 (DCC) 
• R-Value Work: 
  0.128 (Depositor), 0.132 (DCC) 
• R-Value Observed: 
  0.130 (Depositor) 

Literature

Lmo2764 protein, a putative N-acetylmannosamine kinase, from Listeria monocytogenes.

Osipiuk, J., Mack, J., Endres, M., Salazar, J., Zhang, W., 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: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 32.89 kDa 
• Atom Count: 2,674 
• Modeled Residue Count: 291 
• Deposited Residue Count: 297 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-glucoside kinase	A	297	Listeria monocytogenes EGD-e	Mutation(s): 0  Gene Names: bglK, lmo2764 EC: 2.7.1.85
UniProt
Find proteins for Q8Y3R9 (Listeria monocytogenes serovar 1/2a (strain ATCC BAA-679 / EGD-e)) Explore Q8Y3R9  Go to UniProtKB:  Q8Y3R9

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	B [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-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: 1.64 Å
• R-Value Free:  0.169 (Depositor), 0.171 (DCC) 
• R-Value Work:  0.128 (Depositor), 0.132 (DCC) 
• R-Value Observed: 0.130 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M34HTL

Space Group: F 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 87.694	α = 90
b = 121.989	β = 90
c = 153.297	γ = 90

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
SHELXD	phasing
MLPHARE	phasing
DM	phasing
SOLVE	phasing
RESOLVE	phasing
HKL-3000	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-11-14 
Deposition Author(s): Osipiuk, J., Mack, J., Endres, M., Salazar, J., Zhang, W., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2012-11-14
  Type: Initial release
  
• Version 1.1: 2017-11-15
  Changes: Refinement description
• Version 1.2: 2024-11-20
  Changes: Data collection, Database references, Derived calculations, Structure summary