2GBZ

The Crystal Structure of XC847 from Xanthomonas campestris: a 3-5 Oligoribonuclease of DnaQ fold family with a Novel Opposingly-Shifted Helix

• PDB DOI: https://doi.org/10.2210/pdb2GBZ/pdb

• Classification: HYDROLASE
• Organism(s): Xanthomonas campestris pv. campestris
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2006-03-12 Released: 2007-01-16 
• Deposition Author(s): Chin, K.H., Yang, C.Y., Chou, C.C., Wang, A.H.J., Chou, S.H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.263 (Depositor) 
• R-Value Work: 
  0.203 (Depositor) 
• R-Value Observed: 
  0.203 (Depositor) 

Literature

The crystal structure of XC847 from Xanthomonas campestris: a 3'-5' oligoribonuclease of DnaQ fold family with a novel opposingly shifted helix

Chin, K.H., Yang, C.Y., Chou, C.C., Wang, A.H.J., Chou, S.H.

(2006) Proteins 65: 1036-1040

• PubMed: 17029243 
• DOI: https://doi.org/10.1002/prot.21148
• Primary Citation of Related Structures:  
  2GBZ

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Organizational Affiliation: 

Institute of Biochemistry, National Chung-Hsing University, Taichung 40227, Taiwan, Republic of China.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 generated by PISA,PQS (software)

Macromolecule Content

• Total Structure Weight: 21.83 kDa 
• Atom Count: 1,503 
• Modelled Residue Count: 179 
• Deposited Residue Count: 194 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Oligoribonuclease	A	194	Xanthomonas campestris pv. campestris	Mutation(s): 0  EC: 3.1 (PDB Primary Data), 3.1.15 (UniProt)
UniProt
Find proteins for Q8P8S1 (Xanthomonas campestris pv. campestris (strain ATCC 33913 / DSM 3586 / NCPPB 528 / LMG 568 / P 25)) Explore Q8P8S1  Go to UniProtKB:  Q8P8S1

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MG	B [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.263 (Depositor) 
• R-Value Work:  0.203 (Depositor) 
• R-Value Observed: 0.203 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.54	α = 90
b = 67.54	β = 90
c = 89.82	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-01-16 
Deposition Author(s): Chin, K.H., Yang, C.Y., Chou, C.C., Wang, A.H.J., Chou, S.H.

Revision History  

• Version 1.0: 2007-01-16
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance
• Version 1.3: 2017-10-18
  Changes: Refinement description
• Version 1.4: 2024-11-13
  Changes: Data collection, Database references, Derived calculations, Structure summary