4YRH | pdb_00004yrh

p21 isoform of MEC-17 from Danio Rerio

• PDB DOI: https://doi.org/10.2210/pdb4YRH/pdb

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


• Deposited: 2015-03-15 Released: 2015-07-01 
• Deposition Author(s): Xue, T.
• Funding Organization(s): Tianjin Natural Science Foundation

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.86 Å
• R-Value Free: 
  0.256 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.218 (Depositor), 0.231 (DCC) 
• R-Value Observed: 
  0.221 (Depositor) 

Literature

Structure of DrMEC-17 residue 2-185 at 2.85 Angstroms resolution

Xue, T.

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)

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 43.87 kDa 
• Atom Count: 2,923 
• Modeled Residue Count: 349 
• Deposited Residue Count: 368 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Alpha-tubulin N-acetyltransferase 1	A, B	184	Danio rerio	Mutation(s): 0  Gene Names: atat1, mec17 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	C [auth A], E [auth B]	ACETYL COENZYME *A C23 H38 N7 O17 P3 S ZSLZBFCDCINBPY-ZSJPKINUSA-N
EPE	D [auth A], F [auth B]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C8 H18 N2 O4 S JKMHFZQWWAIEOD-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.86 Å
• R-Value Free:  0.256 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.218 (Depositor), 0.231 (DCC) 
• R-Value Observed: 0.221 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.374	α = 90
b = 66.299	β = 103.84
c = 75.841	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data processing
HKL-2000	data scaling
Coot	model building

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2015-07-01 
Deposition Author(s): Xue, T.

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Funding Organization	Location	Grant Number
Tianjin Natural Science Foundation	China	grant 14JCQNJC09300

Revision History  

• Version 1.0: 2015-07-01
  Type: Initial release
  
• Version 1.1: 2024-10-30
  Changes: Data collection, Database references, Derived calculations, Source and taxonomy, Structure summary