5T8T | pdb_00005t8t

Crystal Structure of a S-adenosylmethionine Synthase from Neisseria gonorrhoeae with bound AMP and Magnesium

• PDB DOI: https://doi.org/10.2210/pdb5T8T/pdb

• Classification: TRANSFERASE
• Organism(s): Neisseria gonorrhoeae FA 1090
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2016-09-08 Released: 2016-09-28 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.205 (Depositor), 0.206 (DCC) 
• R-Value Work: 
  0.170 (Depositor), 0.171 (DCC) 
• R-Value Observed: 
  0.172 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of a S-adenosylmethionine Synthase from Neisseria gonorrhoeae with bound AMP and Magnesium

Dranow, D.M., Delker, S.L., Lorimer, D.D., Edwards, T.E.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 86.41 kDa 
• Atom Count: 6,078 
• Modeled Residue Count: 754 
• Deposited Residue Count: 794 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
S-adenosylmethionine synthase	A, B	397	Neisseria gonorrhoeae FA 1090	Mutation(s): 0  Gene Names: metK, NGO0106 EC: 2.5.1.6
UniProt
Find proteins for Q5FAC0 (Neisseria gonorrhoeae (strain ATCC 700825 / FA 1090)) Explore Q5FAC0  Go to UniProtKB:  Q5FAC0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AMP	C [auth B]	ADENOSINE MONOPHOSPHATE C10 H14 N5 O7 P UDMBCSSLTHHNCD-KQYNXXCUSA-N
MG	D [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.205 (Depositor), 0.206 (DCC) 
• R-Value Work:  0.170 (Depositor), 0.171 (DCC) 
• R-Value Observed: 0.172 (Depositor) 

Space Group: P 4₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 116.58	α = 90
b = 116.58	β = 90
c = 145.6	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-09-28 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History  

• Version 1.0: 2016-09-28
  Type: Initial release
  
• Version 1.1: 2016-10-05
  Changes: Data collection
• Version 1.2: 2023-10-04
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.3: 2025-10-22
  Changes: Structure summary