5HK8 | pdb_00005hk8

Crystal structure of a methylesterase protein MES16 from Arabidopsis

• PDB DOI: https://doi.org/10.2210/pdb5HK8/pdb

• Classification: HYDROLASE
• Organism(s): Arabidopsis thaliana
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2016-01-13 Released: 2016-05-04 
• Deposition Author(s): Li, H., Pu, H.
• Funding Organization(s): national natural science fundation of China

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 
  0.246 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.206 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.208 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of a methylesterase protein MES16 from Arabidopsis

Li, H., Pu, H.

(2016) Biochem Biophys Res Commun 

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Biological Assembly 2  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Macromolecule Content 

• Total Structure Weight: 197.24 kDa 
• Atom Count: 11,383 
• Modeled Residue Count: 1,416 
• Deposited Residue Count: 1,788 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Probable pheophorbidase	A, B, C, D, E, F	298	Arabidopsis thaliana	Mutation(s): 0  Gene Names: PPD, MES16, At4g16690, dl4370c, FCAALL.12 EC: 3.1.1.82 (PDB Primary Data), 3.1.1 (UniProt)
UniProt
Find proteins for O23512 (Arabidopsis thaliana) Explore O23512  Go to UniProtKB:  O23512

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free:  0.246 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.206 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.208 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 149.642	α = 90
b = 176.362	β = 90
c = 168.445	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2016-05-04 
Deposition Author(s): Li, H., Pu, H.

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Funding Organization	Location	Grant Number
national natural science fundation of China	China	31300634

Revision History  

• Version 1.0: 2016-05-04
  Type: Initial release
  
• Version 1.1: 2020-09-09
  Changes: Database references, Derived calculations, Structure summary
• Version 1.2: 2023-11-08
  Changes: Data collection, Database references, Refinement description