5JQC | pdb_00005jqc

Crystal structure putative autolysin from Listeria monocytogenes

• PDB DOI: https://doi.org/10.2210/pdb5JQC/pdb

• Classification: HYDROLASE
• Organism(s): Listeria monocytogenes EGD-e
• Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
• Mutation(s): No 


• Deposited: 2016-05-04 Released: 2016-05-18 
• Deposition Author(s): Chang, C., Zhou, M., Shatsman, S., 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: 2.15 Å
• R-Value Free: 
  0.252 (Depositor), 0.259 (DCC) 
• R-Value Work: 
  0.196 (Depositor), 0.203 (DCC) 
• R-Value Observed: 
  0.198 (Depositor) 

Literature

Crystal structure putative autolysin from Listeria monocytogenes

Chang, C., Zhou, M., Shatsman, S., Anderson, W.F., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content 

• Total Structure Weight: 29.71 kDa 
• Atom Count: 2,038 
• Modeled Residue Count: 248 
• Deposited Residue Count: 259 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lmo1076 protein	A	259	Listeria monocytogenes EGD-e	Mutation(s): 0  Gene Names: lmo1076
UniProt
Find proteins for Q8Y842 (Listeria monocytogenes serovar 1/2a (strain ATCC BAA-679 / EGD-e)) Explore Q8Y842  Go to UniProtKB:  Q8Y842

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PEG	H [auth A], I [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
SO4	E [auth A], F [auth A], G [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	B [auth A], C [auth A], D [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-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: 2.15 Å
• R-Value Free:  0.252 (Depositor), 0.259 (DCC) 
• R-Value Work:  0.196 (Depositor), 0.203 (DCC) 
• R-Value Observed: 0.198 (Depositor) 

Diffraction Data: https://doi.org/10.18430/m35jqc

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 39.468	α = 90
b = 89.323	β = 90
c = 94.441	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
SCALEPACK	data scaling
PDB_EXTRACT	data extraction
HKL-3000	data reduction
HKL-3000	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-05-18 
Deposition Author(s): Chang, C., Zhou, M., Shatsman, S., Anderson, W.F., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History  

• Version 1.0: 2016-05-18
  Type: Initial release
  
• Version 1.1: 2018-01-24
  Changes: Database references, Derived calculations
• Version 1.2: 2024-12-25
  Changes: Advisory, Data collection, Database references, Derived calculations, Structure summary