4HKF | pdb_00004hkf

Crystal structure of Danio rerio MEC-17 catalytic domain in complex with acetyl-CoA

• PDB DOI: https://doi.org/10.2210/pdb4HKF/pdb

• Classification: TRANSFERASE
• Organism(s): Danio rerio
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2012-10-15 Released: 2012-12-12 
• Deposition Author(s): Li, W., Zhong, C., Sun, B., Xu, S., Zhang, T., Ding, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.193 (Depositor), 0.141 (DCC) 
• R-Value Work: 
  0.145 (Depositor), 0.148 (DCC) 
• R-Value Observed: 
  0.147 (Depositor) 

Literature

Molecular basis of the acetyltransferase activity of MEC-17 towards alpha- tubulin

Li, W., Zhong, C., Li, L., Sun, B., Wang, W., Xu, S., Zhang, T., Wang, C., Bao, L., Ding, J.

(2012) Cell Res 22: 1707-1711

• PubMed: 23128673 
• DOI: https://doi.org/10.1038/cr.2012.154
• Primary Citation Related Structures: 
  4HKF

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: 22.69 kDa 
• Atom Count: 1,669 
• Modeled Residue Count: 170 
• Deposited Residue Count: 191 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Alpha-tubulin N-acetyltransferase	A	191	Danio rerio	Mutation(s): 0  Gene Names: atat1, mec17, si:ch211-152p11.5, zgc:65893 EC: 2.3.1.108
UniProt
Find proteins for Q6PH17 (Danio rerio) Explore Q6PH17  Go to UniProtKB:  Q6PH17

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ACO	B [auth A]	ACETYL COENZYME *A C23 H38 N7 O17 P3 S ZSLZBFCDCINBPY-ZSJPKINUSA-N
SO4	C [auth A], D [auth A], E [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

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: 1.70 Å
• R-Value Free:  0.193 (Depositor), 0.141 (DCC) 
• R-Value Work:  0.145 (Depositor), 0.148 (DCC) 
• R-Value Observed: 0.147 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.627	α = 90
b = 65.874	β = 90
c = 104.674	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-12-12 
Deposition Author(s): Li, W., Zhong, C., Sun, B., Xu, S., Zhang, T., Ding, J.

Revision History  

• Version 1.0: 2012-12-12
  Type: Initial release
  
• Version 1.1: 2024-10-30
  Changes: Data collection, Database references, Derived calculations, Structure summary