4Q0V

Crystal structure of Acinetobacter sp. DL28 L-ribose isomerase mutant E204Q in complex with L-ribulose

• PDB DOI: https://doi.org/10.2210/pdb4Q0V/pdb

• Classification: ISOMERASE
• Organism(s): Acinetobacter sp. DL-28
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2014-04-02 Released: 2014-05-28 
• Deposition Author(s): Yoshida, H., Yoshihara, A., Teraoka, M., Izumori, K., Kamitori, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.98 Å
• R-Value Free: 0.243 
• R-Value Work: 0.203 
• R-Value Observed: 0.203 

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: 30.02 kDa 
• Atom Count: 2,109 
• Modelled Residue Count: 249 
• Deposited Residue Count: 260 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
L-Ribose isomerase	A	260	Acinetobacter sp. DL-28	Mutation(s): 1  Gene Names: L-RI EC: 5.3.1
UniProt
Find proteins for Q93UQ5 (Acinetobacter sp. DL-28) Explore Q93UQ5  Go to UniProtKB:  Q93UQ5

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NCO	J [auth A]	COBALT HEXAMMINE(III) Co H18 N6 DYLMFCCYOUSRTK-UHFFFAOYSA-N
RUU	D [auth A], F [auth A], G [auth A], H [auth A], I [auth A]	alpha-L-ribulofuranose C5 H10 O5 LQXVFWRQNMEDEE-VAYJURFESA-N
QDK	C [auth A], E [auth A]	L-ribulose C5 H10 O5 ZAQJHHRNXZUBTE-UCORVYFPSA-N
CO	B [auth A]	COBALT (II) ION Co XLJKHNWPARRRJB-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.98 Å
• R-Value Free: 0.243 
• R-Value Work: 0.203 
• R-Value Observed: 0.203 
• Space Group: F 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 95.85	α = 90
b = 107.35	β = 90
c = 118.18	γ = 90

Software Package:

Software Name	Purpose
CrystalClear	data collection
MOLREP	phasing
CNS	refinement
CrystalClear	data reduction
CrystalClear	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-05-28 
Deposition Author(s): Yoshida, H., Yoshihara, A., Teraoka, M., Izumori, K., Kamitori, S.

Revision History  

• Version 1.0: 2014-05-28
  Type: Initial release
  
• Version 1.1: 2014-06-11
  Changes: Database references
• Version 1.2: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Database references, Derived calculations
• Version 1.3: 2022-08-24
  Changes: Database references, Structure summary
• Version 1.4: 2023-11-08
  Changes: Data collection, Refinement description