4L0O | pdb_00004l0o

Structure determination of cystathionine gamma-synthase from Helicobacter pylori

• PDB DOI: https://doi.org/10.2210/pdb4L0O/pdb

• Classification: LYASE
• Organism(s): Helicobacter pylori 26695
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2013-05-31 Released: 2013-12-25 
• Deposition Author(s): Tarique, K.F., Rehman, S.A.A., Gourinath, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.76 Å
• R-Value Free: 
  0.278 (Depositor), 0.261 (DCC) 
• R-Value Work: 
  0.234 (Depositor), 0.221 (DCC) 
• R-Value Observed: 
  0.236 (Depositor) 

Starting Model: experimental

Literature

Structure determination of cystathionine gamma-synthase from Helicobacter pylori

Tarique, K.F., Rehman, S.A.A., Ahmed, E., Gourinath, S.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 8-mer - A8 

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 2 generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 3 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 339.71 kDa 
• Atom Count: 22,365 
• Modeled Residue Count: 2,941 
• Deposited Residue Count: 3,104 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cystathionine gamma-synthase	A [auth H], B [auth A], C, D [auth E], E [auth G], F [auth K], G [auth M], H [auth O]	388	Helicobacter pylori 26695	Mutation(s): 0  Gene Names: cystathionine gamma-synthase, HP_0106, metB EC: 2.5.1.48
UniProt
Find proteins for P56069 (Helicobacter pylori (strain ATCC 700392 / 26695)) Explore P56069  Go to UniProtKB:  P56069

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PLP	I [auth H], J [auth A], K [auth C], L [auth E], M [auth G], O [auth M], P [auth O]	PYRIDOXAL-5'-PHOSPHATE C8 H10 N O6 P NGVDGCNFYWLIFO-UHFFFAOYSA-N
PO4	N [auth K]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.76 Å
• R-Value Free:  0.278 (Depositor), 0.261 (DCC) 
• R-Value Work:  0.234 (Depositor), 0.221 (DCC) 
• R-Value Observed: 0.236 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 115.812	α = 90
b = 174.89	β = 90
c = 324.755	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-12-25 
Deposition Author(s): Tarique, K.F., Rehman, S.A.A., Gourinath, S.

Revision History  

• Version 1.0: 2013-12-25
  Type: Initial release
  
• Version 1.1: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Refinement description