1YPX

Crystal Structure of the Putative Vitamin-B12 Independent Methionine Synthase from Listeria monocytogenes, Northeast Structural Genomics Target LmR13

• PDB DOI: https://doi.org/10.2210/pdb1YPX/pdb

• Classification: TRANSFERASE
• Organism(s): Listeria monocytogenes EGD-e
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2005-01-31 Released: 2005-02-08 
• Deposition Author(s): Forouhar, F., Chen, Y., Benach, J., Xiao, R., Acton, T.B., Montelione, G.T., Hunt, J.F., Tong, L., Northeast Structural Genomics Consortium (NESG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.308 
• R-Value Work: 0.233 
• R-Value Observed: 0.233 

Literature

Crystal Structure of Putative Vitamin-B12 Independent Methionine Synthase from Listeria monocytogenes, Northeast Structural Genomics Target LmR13

Forouhar, F., Chen, Y., Benach, J., Xiao, R., Acton, T.B., Montelione, G.T., Hunt, J.F., Tong, L.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 43.21 kDa 
• Atom Count: 2,627 
• Modelled Residue Count: 318 
• Deposited Residue Count: 375 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
putative vitamin-B12 independent methionine synthase family protein	A	375	Listeria monocytogenes EGD-e	Mutation(s): 4  Gene Names: 985330
UniProt
Find proteins for Q8Y8Q1 (Listeria monocytogenes serovar 1/2a (strain ATCC BAA-679 / EGD-e)) Explore Q8Y8Q1  Go to UniProtKB:  Q8Y8Q1

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4	B [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.308 
• R-Value Work: 0.233 
• R-Value Observed: 0.233 
• Space Group: I 4₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 139.109	α = 90
b = 139.109	β = 90
c = 38.535	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
SnB	phasing
SOLVE	phasing
RESOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-02-08 
Deposition Author(s): Forouhar, F., Chen, Y., Benach, J., Xiao, R., Acton, T.B., Montelione, G.T., Hunt, J.F., Tong, L., Northeast Structural Genomics Consortium (NESG)

Revision History  

• Version 1.0: 2005-02-08
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 1.3: 2017-10-11
  Changes: Refinement description