3CDK | pdb_00003cdk

Crystal structure of the co-expressed succinyl-CoA transferase A and B complex from Bacillus subtilis

• PDB DOI: https://doi.org/10.2210/pdb3CDK/pdb

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


• Deposited: 2008-02-27 Released: 2008-03-18 
• Deposition Author(s): Kim, Y., Zhou, M., Stols, L., Eschenfeldt, W., Donnelly, M., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.59 Å
• R-Value Free: 
  0.253 (Depositor), 0.252 (DCC) 
• R-Value Work: 
  0.193 (Depositor), 0.193 (DCC) 
• R-Value Observed: 
  0.196 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of the co-expressed succinyl-CoA transferase A and B complex from Bacillus subtilis.

Kim, Y., Zhou, M., Stols, L., Eschenfeldt, W., Donnelly, M., Joachimiak, A.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 98.67 kDa 
• Atom Count: 6,720 
• Modeled Residue Count: 870 
• Deposited Residue Count: 920 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Succinyl-CoA:3-ketoacid-coenzyme A transferase subunit A	A, C	241	Bacillus subtilis	Mutation(s): 0  Gene Names: scoA, yxjD, BSU38990, N15K EC: 2.8.3.5
UniProt
Find proteins for P42315 (Bacillus subtilis (strain 168)) Explore P42315  Go to UniProtKB:  P42315

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Succinyl-CoA:3-ketoacid-coenzyme A transferase subunit B	B, D	219	Bacillus subtilis	Mutation(s): 0  Gene Names: scoB, yxjE, BSU38980, N15L EC: 2.8.3.5
UniProt
Find proteins for P42316 (Bacillus subtilis (strain 168)) Explore P42316  Go to UniProtKB:  P42316

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.59 Å
• R-Value Free:  0.253 (Depositor), 0.252 (DCC) 
• R-Value Work:  0.193 (Depositor), 0.193 (DCC) 
• R-Value Observed: 0.196 (Depositor) 

Space Group: P 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.337	α = 90
b = 70.404	β = 106.31
c = 97.996	γ = 90

Software Package:

Software Name	Purpose
MOLREP	phasing
Coot	model building
REFMAC	refinement
SBC-Collect	data collection
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-03-18 
Deposition Author(s): Kim, Y., Zhou, M., Stols, L., Eschenfeldt, W., Donnelly, M., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2008-03-18
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-08-30
  Changes: Data collection, Database references, Refinement description