4MY0 | pdb_00004my0

Crystal Structure of GCN5-related N-acetyltransferase from Kribbella flavida

• PDB DOI: https://doi.org/10.2210/pdb4MY0/pdb

• Classification: TRANSFERASE
• Organism(s): Kribbella flavida DSM 17836
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2013-09-26 Released: 2013-11-06 
• Deposition Author(s): Kim, Y., Mack, J., Endres, M., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.202 (Depositor), 0.203 (DCC) 
• R-Value Work: 
  0.166 (Depositor), 0.168 (DCC) 
• R-Value Observed: 
  0.168 (Depositor) 

Literature

Crystal Structure of GCN5-related N-acetyltransferase from Kribbella flavida

Kim, Y., Mack, J., Endres, M., Joachimiak, A.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D3  (Explore in 3D)
Global Stoichiometry: Homo 6-mer - A6 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 3 generated by PISA (software)

Biological Assembly 4  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 4 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 260.97 kDa 
• Atom Count: 18,874 
• Modeled Residue Count: 2,323 
• Deposited Residue Count: 2,352 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GCN5-related N-acetyltransferase	A, B, C, D, E, F	392	Kribbella flavida DSM 17836	Mutation(s): 0  Gene Names: Kfla_4406
UniProt
Find proteins for D2PVF8 (Kribbella flavida (strain DSM 17836 / JCM 10339 / NBRC 14399)) Explore D2PVF8  Go to UniProtKB:  D2PVF8

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AC8	L [auth C]	[(2R,3R,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-bis(phosphonooxy)tetrahydrofuran-2-yl]methyl (3R)-3-hydroxy-2,2-dimethyl-4-oxo-4-({3-oxo-3-[(2-sulfanylethyl)amino]propyl}amino)butyl dihydrogen diphosphate C21 H37 N7 O19 P4 S SAXULFDJRFDTDN-IBOSZNHHSA-N
ACO	G [auth A], J [auth B], N [auth D], P [auth E], S [auth F]	ACETYL COENZYME *A C23 H38 N7 O17 P3 S ZSLZBFCDCINBPY-ZSJPKINUSA-N
TRS	H [auth A], K [auth B], M [auth C], O [auth D], Q [auth E], T [auth F]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C4 H12 N O3 LENZDBCJOHFCAS-UHFFFAOYSA-O
GOL	I [auth A], R [auth E]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.202 (Depositor), 0.203 (DCC) 
• R-Value Work:  0.166 (Depositor), 0.168 (DCC) 
• R-Value Observed: 0.168 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 92.138	α = 90
b = 166.518	β = 90
c = 183.613	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: 2013-11-06 
Deposition Author(s): Kim, Y., Mack, J., Endres, M., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2013-11-06
  Type: Initial release
  
• Version 1.1: 2024-10-09
  Changes: Data collection, Database references, Derived calculations, Structure summary