3SQZ | pdb_00003sqz

Crystal structure of HMG_CoA synthase complexed with CoA

• PDB DOI: https://doi.org/10.2210/pdb3SQZ/pdb

• Classification: TRANSFERASE
• Organism(s): Streptococcus mutans
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2011-07-06 Released: 2012-07-11 
• Deposition Author(s): Liu, Y.H., Fu, T.M., Liu, X., Su, X.D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.20 Å
• R-Value Free: 
  0.155 (Depositor), 0.152 (DCC) 
• R-Value Work: 
  0.137 (Depositor), 0.136 (DCC) 
• R-Value Observed: 
  0.137 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of HMG-CoA synthase from Streptococcus mutans

Liu, Y.H., Fu, T.M., Liu, X., Su, X.D.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 48.17 kDa 
• Atom Count: 3,468 
• Modeled Residue Count: 389 
• Deposited Residue Count: 426 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative hydroxymethylglutaryl-CoA synthase	A	425	Streptococcus mutans	Mutation(s): 1  Gene Names: SMU_943c EC: 2.3.3.10
UniProt
Find proteins for Q8DUI5 (Streptococcus mutans serotype c (strain ATCC 700610 / UA159)) Explore Q8DUI5  Go to UniProtKB:  Q8DUI5

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
COA	D [auth A]	COENZYME A C21 H36 N7 O16 P3 S RGJOEKWQDUBAIZ-IBOSZNHHSA-N
GOL	B [auth A], C [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSD	A	L-PEPTIDE LINKING	C3 H7 N O4 S		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.20 Å
• R-Value Free:  0.155 (Depositor), 0.152 (DCC) 
• R-Value Work:  0.137 (Depositor), 0.136 (DCC) 
• R-Value Observed: 0.137 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 115.648	α = 90
b = 56.058	β = 117.33
c = 67.365	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
MOLREP	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-07-11 
Deposition Author(s): Liu, Y.H., Fu, T.M., Liu, X., Su, X.D.

Revision History  

• Version 1.0: 2012-07-11
  Type: Initial release
  
• Version 1.1: 2014-02-05
  Changes: Atomic model
• Version 1.2: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.3: 2024-11-20
  Changes: Structure summary