3DMY | pdb_00003dmy

Crystal Structure of a predicated acyl-CoA synthetase from E.coli

• PDB DOI: https://doi.org/10.2210/pdb3DMY/pdb

• Classification: structural genomics, unknown function
• Organism(s): Escherichia coli K-12
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-07-01 Released: 2008-08-05 
• Deposition Author(s): Sugadev, R., Burley, S.K., Swaminathan, S., New York SGX Research Center for Structural Genomics (NYSGXRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.07 Å
• R-Value Free: 
  0.270 (Depositor), 0.270 (DCC) 
• R-Value Work: 
  0.237 (Depositor), 0.240 (DCC) 
• R-Value Observed: 
  0.237 (Depositor) 

Literature

Crystal Structure of a predicted Acyl-CoA-synthetase from E.coli

Sugadev, R., Burley, S.K., Swaminathan, S.

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)

Macromolecule Content

• Total Structure Weight: 102.24 kDa 
• Atom Count: 6,952 
• Modelled Residue Count: 893 
• Deposited Residue Count: 960 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein fdrA	A, B	480	Escherichia coli K-12	Mutation(s): 0  Gene Names: fdrA, ylbD, b0518, JW0506 EC: 2.1.3.5
UniProt
Find proteins for Q47208 (Escherichia coli (strain K12)) Explore Q47208  Go to UniProtKB:  Q47208

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.07 Å
• R-Value Free:  0.270 (Depositor), 0.270 (DCC) 
• R-Value Work:  0.237 (Depositor), 0.240 (DCC) 
• R-Value Observed: 0.237 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.574	α = 90
b = 107.776	β = 90
c = 153.605	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
Blu-Ice	data collection
HKL-2000	data reduction
HKL-2000	data scaling
SHELX	phasing
SOLVE	phasing
SHARP	phasing
ARP	model building
WARP	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-08-05 
Deposition Author(s): Sugadev, R., Burley, S.K., Swaminathan, S., New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History  

• Version 1.0: 2008-08-05
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 1.2: 2017-10-25
  Changes: Refinement description
• Version 1.3: 2021-02-10
  Changes: Database references, Derived calculations, Structure summary
• Version 1.4: 2024-10-30
  Changes: Data collection, Database references, Structure summary