3E6G

Crystal structure of XometC, a cystathionine c-lyase-like protein from Xanthomonas oryzae pv.oryzae

• PDB DOI: https://doi.org/10.2210/pdb3E6G/pdb

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


• Deposited: 2008-08-15 Released: 2009-08-18 
• Deposition Author(s): Ngo, H.P.T., Kim, J.K., Kim, H.S., Jung, J.H., Ahn, Y.J., Kim, J.G., Lee, B.M., Kang, H.W., Kang, L.W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 
  0.295 (Depositor), 0.300 (DCC) 
• R-Value Work: 
  0.216 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.220 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of XometC, a cystathionine c-lyase-like protein from Xanthomonas oryzae pv.oryzae

Ngo, H.P.T., Kim, J.K., Kim, H.S., Jung, J.H., Ahn, Y.J., Kim, J.G., Lee, B.M., Kang, H.W., Kang, L.W.

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: 171.67 kDa 
• Atom Count: 10,661 
• Modelled Residue Count: 1,407 
• Deposited Residue Count: 1,600 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cystathionine gamma-lyase-like protein	A, B, C, D	400	Xanthomonas oryzae pv. oryzae	Mutation(s): 0  Gene Names: metB, XOO0778
UniProt
Find proteins for Q5H4T8 (Xanthomonas oryzae pv. oryzae (strain KACC10331 / KXO85)) Explore Q5H4T8  Go to UniProtKB:  Q5H4T8

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free:  0.295 (Depositor), 0.300 (DCC) 
• R-Value Work:  0.216 (Depositor), 0.220 (DCC) 
• R-Value Observed: 0.220 (Depositor) 

Space Group: P 4₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.351	α = 90
b = 78.351	β = 90
c = 300.989	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
PHASES	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-08-18 
Deposition Author(s): Ngo, H.P.T., Kim, J.K., Kim, H.S., Jung, J.H., Ahn, Y.J., Kim, J.G., Lee, B.M., Kang, H.W., Kang, L.W.

Revision History  

• Version 1.0: 2009-08-18
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-11-01
  Changes: Data collection, Database references, Refinement description