2G3W | pdb_00002g3w

The Crystal Structure of YaeQ Protein from Xanthomonas axonopodis pv. citri

• PDB DOI: https://doi.org/10.2210/pdb2G3W/pdb

• Classification: UNKNOWN FUNCTION
• Organism(s): Xanthomonas citri
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2006-02-21 Released: 2007-02-27 
• Deposition Author(s): Farah, C.S., Guzzo, C.R., Barbosa, J.A.R.G., Nagem, R.A.P.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.247 (Depositor), 0.247 (DCC) 
• R-Value Work: 
  0.192 (Depositor), 0.192 (DCC) 
• R-Value Observed: 
  0.194 (Depositor) 

Literature

Structure of Xanthomonas axonopodis pv. citri YaeQ reveals a new compact protein fold built around a variation of the PD-(D/E)XK nuclease motif

Guzzo, C.R., Nagem, R.A.P., Barbosa, J.A.R.G., Farah, C.S.

(2007) Proteins 69: 644-651

• PubMed: 17623842 
• DOI: https://doi.org/10.1002/prot.21556
• Primary Citation Related Structures: 
  2G3W


• PubMed Abstract: 
  

  The YaeQ family of proteins are found in many Gram-negative and a few Gram-positive bacteria. We have determined the first structure of a member of the YaeQ family by X-ray crystallography. Comparisons with other structures indicate that YaeQ represents a new compact protein fold built around a variation of the PD-(D/E)XK nuclease motif found in type II endonucleases and enzymes involved in DNA replication, repair, and recombination. We show that catalytically important residues in the PD-(D/E)XK nuclease superfamily are spatially conserved in YaeQ and other highly conserved YaeQ residues may be poised to interact with nucleic acid structures.

---

Organizational Affiliation: 
• Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, Avenida Prof. Lineu Prestes 748, São Paulo, SP, CEP 05508-000, Brazil.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 42.1 kDa 
• Atom Count: 3,091 
• Modeled Residue Count: 356 
• Deposited Residue Count: 364 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
hypothetical protein XAC2396	A, B	182	Xanthomonas citri	Mutation(s): 0  Gene Names: XAC2396

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ACT	C [auth A], D [auth A]	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: 1.90 Å
• R-Value Free:  0.247 (Depositor), 0.247 (DCC) 
• R-Value Work:  0.192 (Depositor), 0.192 (DCC) 
• R-Value Observed: 0.194 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 39.766	α = 90
b = 91.969	β = 108.35
c = 48.031	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
SHARP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-02-27 
Deposition Author(s): Farah, C.S., Guzzo, C.R., Barbosa, J.A.R.G., Nagem, R.A.P.

Revision History  

• Version 1.0: 2007-02-27
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.3: 2024-11-06
  Changes: Data collection, Database references, Derived calculations, Structure summary