4Q7A | pdb_00004q7a

Crystal Structure of N-acetyl-ornithine/N-acetyl-lysine Deacetylase from Sphaerobacter thermophilus

• PDB DOI: https://doi.org/10.2210/pdb4Q7A/pdb

• Classification: HYDROLASE
• Organism(s): Sphaerobacter thermophilus DSM 20745
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2014-04-24 Released: 2014-07-02 
• Deposition Author(s): Kim, Y., Tesar, C., Clancy, S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free: 
  0.171 (Depositor), 0.171 (DCC) 
• R-Value Work: 
  0.154 (Depositor), 0.154 (DCC) 
• R-Value Observed: 
  0.156 (Depositor) 

Literature

Crystal Structure of N-acetyl-ornithine/N-acetyl-lysine Deacetylase from Sphaerobacter thermophilus

Kim, Y., Tesar, C., Clancy, S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 8-mer - A8 

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

Macromolecule Content 

• Total Structure Weight: 157.2 kDa 
• Atom Count: 11,552 
• Modeled Residue Count: 1,415 
• Deposited Residue Count: 1,480 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
N-acetyl-ornithine/N-acetyl-lysine deacetylase	A, B, C, D	370	Sphaerobacter thermophilus DSM 20745	Mutation(s): 0  Gene Names: Sthe_0214
UniProt
Find proteins for D1C6B5 (Sphaerobacter thermophilus (strain ATCC 49802 / DSM 20745 / KCCM 41009 / NCIMB 13125 / S 6022)) Explore D1C6B5  Go to UniProtKB:  D1C6B5

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	E [auth A], G [auth B], H [auth B], K [auth D]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	F [auth A], I [auth C], J [auth D], L [auth D]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL	M [auth D]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free:  0.171 (Depositor), 0.171 (DCC) 
• R-Value Work:  0.154 (Depositor), 0.154 (DCC) 
• R-Value Observed: 0.156 (Depositor) 

Space Group: P 4₂

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 119.54	α = 90
b = 119.54	β = 90
c = 119.212	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-07-02 
Deposition Author(s): Kim, Y., Tesar, C., Clancy, S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2014-07-02
  Type: Initial release
  
• Version 1.1: 2024-11-06
  Changes: Data collection, Database references, Derived calculations, Structure summary