3BNM | pdb_00003bnm

Crystal structure of polyamine oxidase FMS1 from Saccharomyces cerevisiae in complex with bis-(3R,3'R)-methylated spermine

• PDB DOI: https://doi.org/10.2210/pdb3BNM/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Saccharomyces cerevisiae
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2007-12-14 Released: 2008-01-29 
• Deposition Author(s): Huang, Q., Hao, Q.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.274 (Depositor) 
• R-Value Work: 
  0.226 (Depositor), 0.224 (DCC) 
• R-Value Observed: 
  0.226 (Depositor) 

Literature

Structural basis of the substrate stereospecificity of FMS1.

Huang, Q., Hao, Q.

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: 119.92 kDa 
• Atom Count: 8,104 
• Modeled Residue Count: 996 
• Deposited Residue Count: 1,032 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Polyamine oxidase FMS1	A [auth B], B [auth A]	516	Saccharomyces cerevisiae	Mutation(s): 0  Gene Names: FMS1, YMR020W, YM9711.09 EC: 1.5.3.11 (PDB Primary Data), 1.5.3.17 (UniProt)
UniProt
Find proteins for P50264 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P50264  Go to UniProtKB:  P50264

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FAD	C [auth B], E [auth A]	FLAVIN-ADENINE DINUCLEOTIDE C27 H33 N9 O15 P2 VWWQXMAJTJZDQX-UYBVJOGSSA-N
SPJ	D [auth B], F [auth A]	(3R,3'R)-N~1~,N~1~'-butane-1,4-diyldibutane-1,3-diamine C12 H30 N4 LXKFTCVCBKNJNM-VXGBXAGGSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.274 (Depositor) 
• R-Value Work:  0.226 (Depositor), 0.224 (DCC) 
• R-Value Observed: 0.226 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 162.237	α = 90
b = 103.969	β = 94.9
c = 77.583	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
DENZO	data reduction
SCALEPACK	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-01-29 
Deposition Author(s): Huang, Q., Hao, Q.

Revision History  

• Version 1.0: 2008-01-29
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2024-11-20
  Changes: Data collection, Database references, Derived calculations, Structure summary