4OVX | pdb_00004ovx

Crystal structure of Xylose isomerase domain protein from Planctomyces limnophilus DSM 3776

• PDB DOI: https://doi.org/10.2210/pdb4OVX/pdb

• Classification: ISOMERASE
• Organism(s): Planctopirus limnophila DSM 3776
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2014-01-22 Released: 2014-02-12 
• Deposition Author(s): Chang, C., Bigelow, L., Endres, M., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free: 
  0.244 (Depositor), 0.249 (DCC) 
• R-Value Work: 
  0.198 (Depositor), 0.205 (DCC) 
• R-Value Observed: 
  0.201 (Depositor) 

Literature

Crystal structure of Xylose isomerase domain protein from Planctomyces limnophilus DSM 3776

Chang, C., Bigelow, L., Endres, M., Joachimiak, A.

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: 31.21 kDa 
• Atom Count: 2,350 
• Modeled Residue Count: 270 
• Deposited Residue Count: 277 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Xylose isomerase domain protein TIM barrel	A	277	Planctopirus limnophila DSM 3776	Mutation(s): 0  Gene Names: Plim_2642
UniProt
Find proteins for D5SQK4 (Planctopirus limnophila (strain ATCC 43296 / DSM 3776 / IFAM 1008 / Mu 290)) Explore D5SQK4  Go to UniProtKB:  D5SQK4

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	B [auth A], C [auth A], D [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-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: 2.25 Å
• R-Value Free:  0.244 (Depositor), 0.249 (DCC) 
• R-Value Work:  0.198 (Depositor), 0.205 (DCC) 
• R-Value Observed: 0.201 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 88.305	α = 90
b = 88.305	β = 90
c = 132.907	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PDB_EXTRACT	data extraction
PHENIX	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-02-12 
Deposition Author(s): Chang, C., Bigelow, L., Endres, M., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2014-02-12
  Type: Initial release
  
• Version 1.1: 2015-02-04
  Changes: Derived calculations
• Version 1.2: 2017-11-22
  Changes: Database references, Derived calculations, Other, Refinement description, Source and taxonomy, Structure summary
• Version 1.3: 2023-12-27
  Changes: Data collection, Database references, Refinement description
• Version 1.4: 2024-11-13
  Changes: Structure summary