2GS8 | pdb_00002gs8

Structure of mevalonate pyrophosphate decarboxylase from Streptococcus pyogenes

• PDB DOI: https://doi.org/10.2210/pdb2GS8/pdb

• Classification: LYASE
• Organism(s): Streptococcus pyogenes M1 GAS
• Expression System: Escherichia coli BL21
• Mutation(s): Yes 


• Deposited: 2006-04-25 Released: 2006-06-06 
• Deposition Author(s): Cuff, M.E., Li, H., Clancy, S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 
  0.194 (Depositor), 0.193 (DCC) 
• R-Value Work: 
  0.165 (Depositor), 0.164 (DCC) 
• R-Value Observed: 
  0.167 (Depositor) 

Literature

Structure of mevalonate pyrophosphate decarboxylase from Streptococcus pyogenes

Cuff, M.E., Li, H., Clancy, S., Joachimiak, A.

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: 36.29 kDa 
• Atom Count: 3,194 
• Modeled Residue Count: 316 
• Deposited Residue Count: 317 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
mevalonate pyrophosphate decarboxylase	A	317	Streptococcus pyogenes M1 GAS	Mutation(s): 13  Gene Names: mvaD EC: 4 (PDB Primary Data), 4.1.1.33 (UniProt)
UniProt
Find proteins for Q9A097 (Streptococcus pyogenes serotype M1) Explore Q9A097  Go to UniProtKB:  Q9A097

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	B [auth A], C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
ACY	K [auth A]	ACETIC ACID C2 H4 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-N

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: 1.50 Å
• R-Value Free:  0.194 (Depositor), 0.193 (DCC) 
• R-Value Work:  0.165 (Depositor), 0.164 (DCC) 
• R-Value Observed: 0.167 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 38.994	α = 90
b = 72.065	β = 90
c = 99.991	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
SBC-Collect	data collection
HKL-2000	data scaling
HKL-3000	phasing
SHELX	phasing
CCP4	phasing
MLPHARE	phasing
DM	phasing
SOLVE	phasing
RESOLVE	phasing
O	model building
ARP/wARP	model building
Coot	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-06-06 
Deposition Author(s): Cuff, M.E., Li, H., Clancy, S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2006-06-06
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.3: 2024-11-20
  Changes: Data collection, Database references, Derived calculations, Structure summary