3CNY | pdb_00003cny

Crystal structure of a putative inositol catabolism protein iole (iole, lp_3607) from lactobacillus plantarum wcfs1 at 1.85 A resolution

• PDB DOI: https://doi.org/10.2210/pdb3CNY/pdb

• Classification: BIOSYNTHETIC PROTEIN
• Organism(s): Lactiplantibacillus plantarum WCFS1
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-03-26 Released: 2008-04-08 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 
  0.210 (Depositor), 0.214 (DCC) 
• R-Value Work: 
  0.165 (Depositor), 0.171 (DCC) 
• R-Value Observed: 
  0.167 (Depositor) 

Literature

Crystal structure of Putative Inositol Catabolism Protein IolE (NP_786806.1) from Lactobacillus plantarum at 1.85 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Biological Assembly 2  

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

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 68.96 kDa 
• Atom Count: 5,618 
• Modeled Residue Count: 600 
• Deposited Residue Count: 602 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Inositol catabolism protein IolE	A, B	301	Lactiplantibacillus plantarum WCFS1	Mutation(s): 0  Gene Names: NP_786806.1, iolE, lp_3607 EC: 4.2.1.44
UniProt
Find proteins for Q88S37 (Lactiplantibacillus plantarum (strain ATCC BAA-793 / NCIMB 8826 / WCFS1)) Explore Q88S37  Go to UniProtKB:  Q88S37

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	C [auth A], D [auth A], F [auth B], G [auth B], H [auth B], I [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
ACT	E [auth B]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free:  0.210 (Depositor), 0.214 (DCC) 
• R-Value Work:  0.165 (Depositor), 0.171 (DCC) 
• R-Value Observed: 0.167 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M33CNY

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.235	α = 90
b = 51.553	β = 90
c = 246.908	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SHELX	phasing
MolProbity	model building
XSCALE	data scaling
PDB_EXTRACT	data extraction
MAR345	data collection
XDS	data reduction
autoSHARP	phasing
SHELXD	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-04-08 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2008-04-08
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: 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
• Version 1.5: 2024-11-06
  Changes: Data collection, Refinement description, Structure summary