2VIA | pdb_00002via

Crystal structure of S172AbsSHMT L-Serine external aldimine

• PDB DOI: https://doi.org/10.2210/pdb2VIA/pdb

• Classification: TRANSFERASE
• Organism(s): Geobacillus stearothermophilus
• Expression System: Escherichia coli BL21
• Mutation(s): Yes 


• Deposited: 2007-11-28 Released: 2007-12-18 
• Deposition Author(s): Rajaram, V., Bhavani, B.S., Prakash, V., Appaji Rao, N., Savithri, H.S., Murthy, M.R.N.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.67 Å
• R-Value Free: 
  0.209 (Depositor), 0.207 (DCC) 
• R-Value Work: 
  0.178 (Depositor), 0.175 (DCC) 
• R-Value Observed: 
  0.179 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of S172Absshmt and its Complexes

Rajaram, V., Bhavani, B.S., Prakash, V., Appaji Rao, N., Savithri, H.S., Murthy, M.R.N.

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 PQS (software)

Macromolecule Content 

• Total Structure Weight: 44.94 kDa 
• Atom Count: 3,626 
• Modeled Residue Count: 405 
• Deposited Residue Count: 405 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SERINE HYDROXYMETHYLTRANSFERASE	A	405	Geobacillus stearothermophilus	Mutation(s): 1  EC: 2.1.2.1
UniProt
Find proteins for Q7SIB6 (Geobacillus stearothermophilus) Explore Q7SIB6  Go to UniProtKB:  Q7SIB6

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PLP	C [auth A]	PYRIDOXAL-5'-PHOSPHATE C8 H10 N O6 P NGVDGCNFYWLIFO-UHFFFAOYSA-N
MPD	D [auth A], E [auth A]	(4S)-2-METHYL-2,4-PENTANEDIOL C6 H14 O2 SVTBMSDMJJWYQN-YFKPBYRVSA-N
SER	B [auth A]	SERINE C3 H7 N O3 MTCFGRXMJLQNBG-REOHCLBHSA-N
PO4	F [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.67 Å
• R-Value Free:  0.209 (Depositor), 0.207 (DCC) 
• R-Value Work:  0.178 (Depositor), 0.175 (DCC) 
• R-Value Observed: 0.179 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.986	α = 90
b = 106.283	β = 90
c = 57.076	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-12-18 
Deposition Author(s): Rajaram, V., Bhavani, B.S., Prakash, V., Appaji Rao, N., Savithri, H.S., Murthy, M.R.N.

Revision History  

• Version 1.0: 2007-12-18
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-12-13
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description