6XBQ | pdb_00006xbq

Streptomyces coelicolor methylmalonyl-CoA epimerase in complex with carboxy-carba(dethia)-CoA

• PDB DOI: https://doi.org/10.2210/pdb6XBQ/pdb

• Classification: ISOMERASE/INHIBITOR
• Organism(s): Streptomyces coelicolor A3(2)
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2020-06-07 Released: 2020-07-01 
• Deposition Author(s): Stunkard, L.M., Boram, T.J., Benjamin, A.B., Bower, J.B., Lohman, J.R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.64 Å
• R-Value Free: 
  0.175 (Depositor), 0.180 (DCC) 
• R-Value Work: 
  0.154 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.155 (Depositor) 

Starting Model: experimental

Literature

Streptomyces coelicolor methylmalonyl-CoA epimerase in complex with carboxy-carba(dethia)-CoA

Stunkard, L.M., Boram, T.J., Benjamin, A.B., Bower, J.B., Lohman, J.R.

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: 17.1 kDa 
• Atom Count: 1,401 
• Modeled Residue Count: 144 
• Deposited Residue Count: 146 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Methylmalonyl-CoA epimerase	A	146	Streptomyces coelicolor A3(2)	Mutation(s): 1  Gene Names: SCO5398
UniProt
Find proteins for Q9L2C2 (Streptomyces coelicolor (strain ATCC BAA-471 / A3(2) / M145)) Explore Q9L2C2  Go to UniProtKB:  Q9L2C2

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CMX (Subject of Investigation/LOI)	E [auth A]	CARBOXYMETHYLDETHIA COENZYME *A C23 H38 N7 O18 P3 SKRDARVCOPFVCP-GRFIIANRSA-N
SO4	C [auth A], D [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
CO	B [auth A]	COBALT (II) ION Co XLJKHNWPARRRJB-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.64 Å
• R-Value Free:  0.175 (Depositor), 0.180 (DCC) 
• R-Value Work:  0.154 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.155 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.504	α = 90
b = 68.504	β = 90
c = 103.315	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
SCALEPACK	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction
ARP/wARP	model building
HKL-2000	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-07-01 
Deposition Author(s): Stunkard, L.M., Boram, T.J., Benjamin, A.B., Bower, J.B., Lohman, J.R.

Revision History  

• Version 1.0: 2020-07-01
  Type: Initial release
  
• Version 1.1: 2023-10-18
  Changes: Data collection, Database references, Refinement description