3VWD | pdb_00003vwd

Crystal structure of alpha-tubulin acetyltransferase domain of human Mec-17 in complex with acetoacetyl-CoA (P21212 form)

• PDB DOI: https://doi.org/10.2210/pdb3VWD/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2012-08-22 Released: 2013-08-28 
• Deposition Author(s): Yuzawa, S., Sumimoto, H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.25 Å
• R-Value Free: 
  0.170 (Depositor), 0.170 (DCC) 
• R-Value Work: 
  0.150 (Depositor), 0.150 (DCC) 
• R-Value Observed: 
  0.151 (Depositor) 

Literature

Crystal structure of alpha-tubulin acetyltransferase domain of human Mec-17

Yuzawa, S., Sumimoto, H.

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: 23.91 kDa 
• Atom Count: 1,881 
• Modeled Residue Count: 196 
• Deposited Residue Count: 201 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Alpha-tubulin N-acetyltransferase	A	201	Homo sapiens	Mutation(s): 0  Gene Names: ATAT1, C6orf134, MEC17, Nbla00487 EC: 2.3.1.108
UniProt & NIH Common Fund Data Resources
Find proteins for Q5SQI0 (Homo sapiens) Explore Q5SQI0  Go to UniProtKB:  Q5SQI0
PHAROS:  Q5SQI0 GTEx:  ENSG00000137343

Small Molecules

Ligands 3 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
EDO	F [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL	C [auth A], D [auth A], E [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.25 Å
• R-Value Free:  0.170 (Depositor), 0.170 (DCC) 
• R-Value Work:  0.150 (Depositor), 0.150 (DCC) 
• R-Value Observed: 0.151 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.175	α = 90
b = 117.464	β = 90
c = 37.38	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-08-28 
Deposition Author(s): Yuzawa, S., Sumimoto, H.

Revision History  

• Version 1.0: 2013-08-28
  Type: Initial release
  
• Version 1.1: 2017-11-22
  Changes: Refinement description
• Version 1.2: 2024-03-20
  Changes: Data collection, Database references, Derived calculations