6AW4 | pdb_00006aw4

1.50A resolution structure of catechol O-methyltransferase (COMT) from Nannospalax galili

• PDB DOI: https://doi.org/10.2210/pdb6AW4/pdb

• Classification: TRANSFERASE
• Organism(s): Nannospalax galili
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2017-09-05 Released: 2018-09-12 
• Deposition Author(s): Lovell, S., Mehzabeen, N., Battaile, K.P., Deng, Y., Hanzlik, R.P., Shams, I., Moskovitz, J.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 
  0.170 (Depositor), 0.177 (DCC) 
• R-Value Work: 
  0.154 (Depositor), 0.165 (DCC) 
• R-Value Observed: 
  0.154 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of the catechol-o-methyl transferase (COMT) enzyme of the subterranean mole rat (Spalax) and the effect of L136M substitution

Deng, Y., Lovell, S., Mehzabeen, N., Battaile, K.P., Hanzlik, R.P., Shams, I., Moskovitz, J.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 26.43 kDa 
• Atom Count: 1,930 
• Modeled Residue Count: 213 
• Deposited Residue Count: 228 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Catechol O-methyltransferase	A	228	Nannospalax galili	Mutation(s): 0  EC: 2.1.1.6
UniProt
Find proteins for A0A452CSQ0 (Nannospalax galili) Explore A0A452CSQ0  Go to UniProtKB:  A0A452CSQ0

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TRS	E [auth A]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C4 H12 N O3 LENZDBCJOHFCAS-UHFFFAOYSA-O
PO4	F [auth A], G [auth A], H [auth A], I [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
GOL	B [auth A], C [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
NA	D [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free:  0.170 (Depositor), 0.177 (DCC) 
• R-Value Work:  0.154 (Depositor), 0.165 (DCC) 
• R-Value Observed: 0.154 (Depositor) 

Space Group: P 6₂

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 94.755	α = 90
b = 94.755	β = 90
c = 75.934	γ = 120

Software Package:

Software Name	Purpose
Aimless	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data processing
XDS	data reduction

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2018-09-12 
Deposition Author(s): Lovell, S., Mehzabeen, N., Battaile, K.P., Deng, Y., Hanzlik, R.P., Shams, I., Moskovitz, J.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	P30 GM110761

Revision History  

• Version 1.0: 2018-09-12
  Type: Initial release
  
• Version 1.1: 2019-02-20
  Changes: Author supporting evidence, Data collection
• Version 1.2: 2020-01-01
  Changes: Author supporting evidence
• Version 1.3: 2023-10-04
  Changes: Data collection, Database references, Refinement description