6LD9 | pdb_00006ld9

Crystal structure of cystathionine gamma synthase from Xanthomonas oryzae pv. oryzae in complex with cystathionine

• PDB DOI: https://doi.org/10.2210/pdb6LD9/pdb

• Classification: BIOSYNTHETIC PROTEIN
• Organism(s): Xanthomonas oryzae pv. oryzae KACC 10331
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2019-11-20 Released: 2020-11-25 
• Deposition Author(s): Ngo, H.P.T., Nguyen, T.D.Q., Kang, L.W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.186 (Depositor), 0.190 (DCC) 
• R-Value Work: 
  0.153 (Depositor), 0.160 (DCC) 
• R-Value Observed: 
  0.154 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of cystathionine gamma synthase from Xanthomonas oryzae pv. oryzae in complex with cystathionine

Ngo, H.P.T., Nguyen, T.D.Q., 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: 174.48 kDa 
• Atom Count: 12,052 
• Modeled Residue Count: 1,549 
• Deposited Residue Count: 1,632 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cystathionine gamma-synthase	A, B, C, D	408	Xanthomonas oryzae pv. oryzae KACC 10331	Mutation(s): 2  Gene Names: metB, XOO1818
UniProt
Find proteins for Q5H1U9 (Xanthomonas oryzae pv. oryzae (strain KACC10331 / KXO85)) Explore Q5H1U9  Go to UniProtKB:  Q5H1U9

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
E9U (Subject of Investigation/LOI)	E [auth A], F [auth B], G [auth C], H [auth D]	(2~{S})-4-[(2~{R})-2-azanyl-3-oxidanyl-3-oxidanylidene-propyl]sulfanyl-2-[(~{E})-[2-methyl-3-oxidanyl-5-(phosphonooxymethyl)pyridin-4-yl]methylideneamino]butanoic acid C15 H22 N3 O9 P S BNRWEPGYMATFEB-QIDXEYLZSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.186 (Depositor), 0.190 (DCC) 
• R-Value Work:  0.153 (Depositor), 0.160 (DCC) 
• R-Value Observed: 0.154 (Depositor) 

Space Group: I 4₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 161.146	α = 90
b = 161.146	β = 90
c = 245.259	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-11-25 
Deposition Author(s): Ngo, H.P.T., Nguyen, T.D.Q., Kang, L.W.

Revision History  

• Version 1.0: 2020-11-25
  Type: Initial release
  
• Version 1.1: 2023-11-22
  Changes: Data collection, Database references, Refinement description