4GS5 | pdb_00004gs5

The crystal structure of acyl-CoA synthetase (AMP-forming)/AMP-acid ligase II-like protein from Dyadobacter fermentans DSM 18053

• PDB DOI: https://doi.org/10.2210/pdb4GS5/pdb

• Classification: LIGASE
• Organism(s): Dyadobacter fermentans DSM 18053
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2012-08-27 Released: 2012-09-12 
• Deposition Author(s): Tan, K., Holowicki, J., Clancy, S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.02 Å
• R-Value Free: 
  0.255 (Depositor), 0.245 (DCC) 
• R-Value Work: 
  0.196 (Depositor), 0.189 (DCC) 
• R-Value Observed: 
  0.198 (Depositor) 

Literature

The crystal structure of acyl-CoA synthetase (AMP-forming)/AMP-acid ligase II-like protein from Dyadobacter fermentans DSM 18053

Tan, K., Holowicki, J., Clancy, S., Joachimiak, A.

To be published.

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 41.93 kDa 
• Atom Count: 2,910 
• Modeled Residue Count: 350 
• Deposited Residue Count: 358 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Acyl-CoA synthetase (AMP-forming)/AMP-acid ligase II-like protein	A	358	Dyadobacter fermentans DSM 18053	Mutation(s): 0  Gene Names: Dfer_1215
UniProt
Find proteins for C6W5A4 (Dyadobacter fermentans (strain ATCC 700827 / DSM 18053 / CIP 107007 / KCTC 52180 / NS114)) Explore C6W5A4  Go to UniProtKB:  C6W5A4

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
IOD	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], K [auth A], L [auth A], M [auth A]	IODIDE ION I XMBWDFGMSWQBCA-UHFFFAOYSA-M
EDO	N [auth A], O [auth A], P [auth A], Q [auth A], R [auth A], S [auth A], T [auth A], U [auth A], V [auth A], W [auth A], X [auth A], Y [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-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: 2.02 Å
• R-Value Free:  0.255 (Depositor), 0.245 (DCC) 
• R-Value Work:  0.196 (Depositor), 0.189 (DCC) 
• R-Value Observed: 0.198 (Depositor) 

Space Group: P 4₃ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.148	α = 90
b = 67.148	β = 90
c = 176.257	γ = 90

Software Package:

Software Name	Purpose
SBC-Collect	data collection
SHELXD	phasing
MLPHARE	phasing
DM	model building
RESOLVE	model building
HKL-3000	phasing
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
DM	phasing
RESOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-09-12 
Deposition Author(s): Tan, K., Holowicki, J., Clancy, S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2012-09-12
  Type: Initial release
  
• Version 1.1: 2024-10-16
  Changes: Data collection, Database references, Derived calculations, Structure summary