4K15 | pdb_00004k15

2.75 Angstrom Crystal Structure of Hypothetical Protein lmo2686 from Listeria monocytogenes EGD-e

• PDB DOI: https://doi.org/10.2210/pdb4K15/pdb

• Classification: UNKNOWN FUNCTION
• Organism(s): Listeria monocytogenes EGD-e
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2013-04-04 Released: 2013-04-17 
• Deposition Author(s): Minasov, G., Wawrzak, Z., Halavaty, A., Shuvalova, L., Dubrovska, I., Winsor, J., Grimshaw, S., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.75 Å
• R-Value Free: 
  0.240 (Depositor), 0.238 (DCC) 
• R-Value Work: 
  0.196 (Depositor), 0.197 (DCC) 
• R-Value Observed: 
  0.198 (Depositor) 

Literature

2.75 Angstrom Crystal Structure of Hypothetical Protein lmo2686 from Listeria monocytogenes EGD-e

Minasov, G., Wawrzak, Z., Halavaty, A., Shuvalova, L., Dubrovska, I., Winsor, J., Grimshaw, S., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C6  (Explore in 3D)
Global Stoichiometry: Homo 6-mer - A6 

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

Macromolecule Content 

• Total Structure Weight: 58.78 kDa 
• Atom Count: 3,195 
• Modeled Residue Count: 398 
• Deposited Residue Count: 525 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lmo2686 protein	A, B, C	175	Listeria monocytogenes EGD-e	Mutation(s): 0  Gene Names: lmo2686
UniProt
Find proteins for Q8Y3Z3 (Listeria monocytogenes serovar 1/2a (strain ATCC BAA-679 / EGD-e)) Explore Q8Y3Z3  Go to UniProtKB:  Q8Y3Z3

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CL	D [auth A], E [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.75 Å
• R-Value Free:  0.240 (Depositor), 0.238 (DCC) 
• R-Value Work:  0.196 (Depositor), 0.197 (DCC) 
• R-Value Observed: 0.198 (Depositor) 

Diffraction Data: https://doi.org/10.18430/m34k15

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 91.093	α = 90
b = 91.093	β = 90
c = 125.47	γ = 120

Software Package:

Software Name	Purpose
Blu-Ice	data collection
PHENIX	model building
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-04-17 
Deposition Author(s): Minasov, G., Wawrzak, Z., Halavaty, A., Shuvalova, L., Dubrovska, I., Winsor, J., Grimshaw, S., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History  

• Version 1.0: 2013-04-17
  Type: Initial release
  
• Version 1.1: 2017-11-15
  Changes: Refinement description
• Version 1.2: 2024-11-06
  Changes: Data collection, Database references, Derived calculations, Structure summary