6UWD | pdb_00006uwd

Crystal structure of Apo AtmM

• PDB DOI: https://doi.org/10.2210/pdb6UWD/pdb

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


• Deposited: 2019-11-05 Released: 2020-11-25 
• Deposition Author(s): Alvarado, S.K., Wang, Z., Miller, M.D., Thorson, J.S., Phillips Jr., G.N.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Science Foundation (NSF, United States)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.04 Å
• R-Value Free: 
  0.208 (Depositor), 0.216 (DCC) 
• R-Value Work: 
  0.188 (Depositor), 0.199 (DCC) 
• R-Value Observed: 
  0.189 (Depositor) 

Starting Model: experimental

Literature

Structure of Apo AtmM

Alvarado, S.K., Miller, M.D., Wang, Z., Thorson, J.S., Phillips Jr., G.N.

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

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 28.75 kDa 
• Atom Count: 2,010 
• Modeled Residue Count: 257 
• Deposited Residue Count: 268 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
D-glucose O-methyltransferase	A	268	Actinomadura melliaura	Mutation(s): 0  Gene Names: atM
UniProt
Find proteins for Q0H2W9 (Actinomadura melliaura) Explore Q0H2W9  Go to UniProtKB:  Q0H2W9

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ACT	B [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
MG	C [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.04 Å
• R-Value Free:  0.208 (Depositor), 0.216 (DCC) 
• R-Value Work:  0.188 (Depositor), 0.199 (DCC) 
• R-Value Observed: 0.189 (Depositor) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 118.62	α = 90
b = 118.62	β = 90
c = 62.443	γ = 120

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2020-11-25 
Deposition Author(s): Alvarado, S.K., Wang, Z., Miller, M.D., Thorson, J.S., Phillips Jr., G.N.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R01 GM115261
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	U01 GM098248
National Science Foundation (NSF, United States)	United States	STC 1231306

Revision History  

• Version 1.0: 2020-11-25
  Type: Initial release
  
• Version 1.1: 2021-09-15
  Changes: Database references, Structure summary
• Version 1.2: 2023-10-11
  Changes: Data collection, Refinement description