3FXA | pdb_00003fxa

Crystal structure of a putative sugar-phosphate isomerase (lmof2365_0531) from listeria monocytogenes str. 4b f2365 at 1.60 A resolution

• PDB DOI: https://doi.org/10.2210/pdb3FXA/pdb

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


• Deposited: 2009-01-20 Released: 2009-02-03 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 
  0.157 (Depositor), 0.140 (DCC) 
• R-Value Work: 
  0.133 (Depositor), 0.140 (DCC) 
• R-Value Observed: 
  0.135 (Depositor) 

Literature

Crystal structure of putative sugar-phosphate isomerase (YP_013136.1) from Listeria monocytogenes 4b F2365 at 1.60 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Macromolecule Content 

• Total Structure Weight: 86.64 kDa 
• Atom Count: 6,305 
• Modeled Residue Count: 766 
• Deposited Residue Count: 804 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SIS domain protein	A, B, C, D	201	Listeria monocytogenes serotype 4b str. F2365	Mutation(s): 0  Gene Names: LMOf2365_0531, YP_013136.1

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	E [auth B], F [auth D]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free:  0.157 (Depositor), 0.140 (DCC) 
• R-Value Work:  0.133 (Depositor), 0.140 (DCC) 
• R-Value Observed: 0.135 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M33FXA

Space Group: P 3₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.944	α = 90
b = 57.944	β = 90
c = 197.964	γ = 120

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
SHELX	phasing
SHARP	phasing
PHASER	phasing
REFMAC	refinement
MolProbity	model building
PDB_EXTRACT	data extraction
MAR345	data collection
SHELXD	phasing
autoSHARP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-02-03 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2009-02-03
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2017-11-01
  Changes: Refinement description
• Version 1.3: 2023-02-01
  Changes: Database references, Derived calculations
• Version 1.4: 2024-11-20
  Changes: Data collection, Refinement description, Structure summary