5I2H

Crystal structure of O-methyltransferase family 2 protein Plim_1147 from Planctomyces limnophilus DSM 3776 complex with Apigenin

• PDB DOI: https://doi.org/10.2210/pdb5I2H/pdb

• Classification: TRANSFERASE
• Organism(s): Planctopirus limnophila DSM 3776
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2016-02-08 Released: 2016-03-02 
• Deposition Author(s): Chang, C., Duke, N., Bigelow, L., Bearden, J., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)
• 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: 1.55 Å
• R-Value Free: 0.197 
• R-Value Work: 0.155 
• R-Value Observed: 0.156 

Literature

Crystal structure of O-methyltransferase family 2 protein Plim_1147 from Planctomyces limnophilus DSM 3776 complex with Apigenin.

Chang, C., Duke, N., Bigelow, L., Bearden, J., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

To be published.

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 81.07 kDa 
• Atom Count: 5,998 
• Modelled Residue Count: 663 
• Deposited Residue Count: 728 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
O-methyltransferase family 2	A, B	364	Planctopirus limnophila DSM 3776	Mutation(s): 0  Gene Names: Plim_1147
UniProt
Find proteins for D5STZ7 (Planctopirus limnophila (strain ATCC 43296 / DSM 3776 / IFAM 1008 / Mu 290)) Explore D5STZ7  Go to UniProtKB:  D5STZ7

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AGI	C [auth A], K [auth B]	5,7-dihydroxy-2-(4-hydroxyphenyl)-4H-chromen-4-one C15 H10 O5 KZNIFHPLKGYRTM-UHFFFAOYSA-N
EDO	D [auth A], E [auth A], F [auth A], G [auth A], L [auth B], M [auth B], N [auth B], O [auth B], P [auth B], Q [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
FMT	H [auth A], I [auth A], J [auth A], R [auth B], S [auth B], T [auth B], U [auth B], V [auth B]	FORMIC ACID C H2 O2 BDAGIHXWWSANSR-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: 1.55 Å
• R-Value Free: 0.197 
• R-Value Work: 0.155 
• R-Value Observed: 0.156 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.516	α = 90
b = 83.192	β = 90
c = 119.099	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
SCALEPACK	data scaling
PDB_EXTRACT	data extraction
HKL-3000	data reduction
HKL-3000	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2016-03-02 
Deposition Author(s): Chang, C., Duke, N., Bigelow, L., Bearden, J., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM115586

Revision History  

• Version 1.0: 2016-03-02
  Type: Initial release
  
• Version 1.1: 2017-09-27
  Changes: Author supporting evidence, Derived calculations
• Version 1.2: 2019-12-25
  Changes: Author supporting evidence