6ULD

Crystal structure of serine hydroxymethyltransferase from Mycobacterium tuberculosis with bound PLP forming a Schiff base with substrate Serine in one monomer and PLP forming a Schiff base with product Glycine in the other monomer

• PDB DOI: https://doi.org/10.2210/pdb6ULD/pdb

• Classification: TRANSFERASE
• Organism(s): Mycobacterium tuberculosis
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2019-10-07 Released: 2019-10-16 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.163 
• R-Value Work: 0.126 
• R-Value Observed: 0.126 

Literature

Crystal structure of serine hydroxymethyltransferase from Mycobacterium tuberculosis with bound PLP forming a Schiff base with substrate Serine in one monomer and PLP forming a Schiff base with product Glycine in the other monomer

Dranow, D.M., Abendroth, J., Lorimer, D.D., Horanyi, P.S., 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)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 95.66 kDa 
• Atom Count: 7,157 
• Modelled Residue Count: 856 
• Deposited Residue Count: 894 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Serine hydroxymethyltransferase	A, B	447	Mycobacterium tuberculosis	Mutation(s): 0  Gene Names: glyA1, glyA, ERS124361_03156 EC: 2.1.2.1

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PLP (Subject of Investigation/LOI)	C [auth A], F [auth B]	PYRIDOXAL-5'-PHOSPHATE C8 H10 N O6 P NGVDGCNFYWLIFO-UHFFFAOYSA-N
MPD	G [auth B], H [auth B]	(4S)-2-METHYL-2,4-PENTANEDIOL C6 H14 O2 SVTBMSDMJJWYQN-YFKPBYRVSA-N
SER (Subject of Investigation/LOI)	E [auth A]	SERINE C3 H7 N O3 MTCFGRXMJLQNBG-REOHCLBHSA-N
GLY (Subject of Investigation/LOI)	D [auth A]	GLYCINE C2 H5 N O2 DHMQDGOQFOQNFH-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.163 
• R-Value Work: 0.126 
• R-Value Observed: 0.126 
• Space Group: P 1 2₁ 1
• Diffraction Data: https://doi.org/10.18430/m36uld

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.65	α = 90
b = 60.01	β = 92.993
c = 101.66	γ = 90

Software Package:

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

Structure Validation

Currently 6ULD does not have a validation slider image.

Entry History 

Deposition Data

• Released Date: 2019-10-16 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History  

• Version 1.0: 2019-10-16
  Type: Initial release
  
• Version 1.1: 2023-10-11
  Changes: Data collection, Database references, Refinement description