5AVP | pdb_00005avp

Crystal structure of Geodermatophilus obscurus L-ribose isomerase

• PDB DOI: https://doi.org/10.2210/pdb5AVP/pdb

• Classification: ISOMERASE
• Organism(s): Geodermatophilus obscurus DSM 43160
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2015-06-29 Released: 2016-06-29 
• Deposition Author(s): Terami, Y., Kamitori, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 
  0.294 (Depositor), 0.290 (DCC) 
• R-Value Work: 
  0.246 (Depositor), 0.250 (DCC) 
• R-Value Observed: 
  0.246 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of Geodermatophilus obscurus L-ribose isomerase

Terami, Y., Kamitori, S.

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: 121.22 kDa 
• Atom Count: 7,635 
• Modeled Residue Count: 960 
• Deposited Residue Count: 1,076 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
L-ribose isomerase	A, B, C, D	269	Geodermatophilus obscurus DSM 43160	Mutation(s): 0  Gene Names: Gobs_2645 EC: 5.3.1
UniProt
Find proteins for D2S5K0 (Geodermatophilus obscurus (strain ATCC 25078 / DSM 43160 / JCM 3152 / CCUG 61914 / KCC A-0152 / KCTC 9177 / NBRC 13315 / NRRL B-3577 / G-20)) Explore D2S5K0  Go to UniProtKB:  D2S5K0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MN	E [auth A], F [auth B], G [auth C], H [auth D]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free:  0.294 (Depositor), 0.290 (DCC) 
• R-Value Work:  0.246 (Depositor), 0.250 (DCC) 
• R-Value Observed: 0.246 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 90.533	α = 90
b = 123.226	β = 97.38
c = 109.446	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-06-29 
Deposition Author(s): Terami, Y., Kamitori, S.

Revision History  

• Version 1.0: 2016-06-29
  Type: Initial release
  
• Version 1.1: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Refinement description