3E5D

Crystal structure of a putative glyoxalase i (lmof2365_0426) from listeria monocytogenes str. 4b f2365 at 2.70 A resolution

• PDB DOI: https://doi.org/10.2210/pdb3E5D/pdb

• Classification: LYASE
• Organism(s): Listeria monocytogenes serotype 4b str. F2365
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-08-13 Released: 2008-08-26 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.198 
• R-Value Work: 0.172 
• R-Value Observed: 0.173 

Literature

Crystal structure of Putative Glyoxalase I (YP_013033.1) from LISTERIA MONOCYTOGENES 4b F2365 at 2.70 A resolution

Joint Center for Structural Genomics (JCSG)

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: 14.5 kDa 
• Atom Count: 1,007 
• Modelled Residue Count: 126 
• Deposited Residue Count: 127 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative Glyoxalase I	A	127	Listeria monocytogenes serotype 4b str. F2365	Mutation(s): 0  Gene Names: LMOf2365_0426

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
UNL	B [auth A]	Unknown ligand

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: 2.70 Å
• R-Value Free: 0.198 
• R-Value Work: 0.172 
• R-Value Observed: 0.173 
• Space Group: I 2₁ 3
• Diffraction Data: https://doi.org/10.18430/M33E5D

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 123.59	α = 90
b = 123.59	β = 90
c = 123.59	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SHELX	phasing
MolProbity	model building
XSCALE	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
SHELXD	phasing
autoSHARP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-08-26 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2008-08-26
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2017-10-25
  Changes: Refinement description
• Version 1.3: 2019-07-24
  Changes: Data collection, Derived calculations, Refinement description
• Version 1.4: 2023-02-01
  Changes: Database references, Derived calculations