5T8S

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.171 
  • R-Value Work: 0.148 
  • R-Value Observed: 0.149 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

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

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

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
S-adenosylmethionine synthase
A, B
397Neisseria gonorrhoeae FA 1090Mutation(s): 0 
Gene Names: metKNGO0106
EC: 2.5.1.6
UniProt
Find proteins for Q5FAC0 (Neisseria gonorrhoeae (strain ATCC 700825 / FA 1090))
Explore Q5FAC0 
Go to UniProtKB:  Q5FAC0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5FAC0
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SAM
Query on SAM

Download Ideal Coordinates CCD File 
I [auth B]S-ADENOSYLMETHIONINE
C15 H22 N6 O5 S
MEFKEPWMEQBLKI-FCKMPRQPSA-N
AMP
Query on AMP

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D [auth A]ADENOSINE MONOPHOSPHATE
C10 H14 N5 O7 P
UDMBCSSLTHHNCD-KQYNXXCUSA-N
3PO
Query on 3PO

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K [auth B]TRIPHOSPHATE
H5 O10 P3
UNXRWKVEANCORM-UHFFFAOYSA-N
POP
Query on POP

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F [auth A]PYROPHOSPHATE 2-
H2 O7 P2
XPPKVPWEQAFLFU-UHFFFAOYSA-L
PO4
Query on PO4

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G [auth A]PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
MG
Query on MG

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C [auth A],
E [auth A],
H [auth B],
J [auth B]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.171 
  • R-Value Work: 0.148 
  • R-Value Observed: 0.149 
  • Space Group: P 41 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 115.71α = 90
b = 115.71β = 90
c = 146.24γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
MR-Rosettaphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2016-09-28
    Type: Initial release
  • Version 1.1: 2023-10-04
    Changes: Data collection, Database references, Derived calculations, Refinement description