3UNV | pdb_00003unv

Pantoea agglomerans Phenylalanine Aminomutase

• PDB DOI: https://doi.org/10.2210/pdb3UNV/pdb

• Classification: LYASE
• Organism(s): Pantoea agglomerans
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2011-11-16 Released: 2012-02-22 
• Deposition Author(s): Geiger, J., Strom, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.54 Å
• R-Value Free: 
  0.247 (Depositor), 0.257 (DCC) 
• R-Value Work: 
  0.204 (Depositor), 0.212 (DCC) 
• R-Value Observed: 
  0.206 (Depositor) 

Literature

Insights into the mechanistic pathway of the Pantoea agglomerans phenylalanine aminomutase.

Strom, S., Wanninayake, U., Ratnayake, N.D., Walker, K.D., Geiger, J.H.

(2012) Angew Chem Int Ed Engl 51: 2898-2902

• PubMed: 22319000 
• DOI: https://doi.org/10.1002/anie.201108525
• Primary Citation Related Structures: 
  3UNV

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Organizational Affiliation: 
• Department of Chemistry, Michigan State University, East Lansing, MI 48824, USA.

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)

Biological Assembly 2  

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

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

Macromolecule Content 

• Total Structure Weight: 122.3 kDa 
• Atom Count: 8,538 
• Modeled Residue Count: 1,028 
• Deposited Residue Count: 1,094 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
AdmH	A, B	547	Pantoea agglomerans	Mutation(s): 0
UniProt
Find proteins for Q84FL5 (Enterobacter agglomerans) Explore Q84FL5  Go to UniProtKB:  Q84FL5

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PHE	D [auth A]	PHENYLALANINE C9 H11 N O2 COLNVLDHVKWLRT-QMMMGPOBSA-N
SFE	C [auth A], M [auth B]	(3S)-3-amino-3-phenylpropanoic acid C9 H11 N O2 UJOYFRCOTPUKAK-QMMMGPOBSA-N
PO4	J [auth A], K [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
GOL	E [auth A], N [auth B], O [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO	F [auth A], G [auth A], H [auth A], I [auth A], L [auth B], P [auth B], Q [auth B], R [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
KWS	A, B	L-PEPTIDE LINKING	C9 H13 N3 O4		THR, SER, GLY

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.54 Å
• R-Value Free:  0.247 (Depositor), 0.257 (DCC) 
• R-Value Work:  0.204 (Depositor), 0.212 (DCC) 
• R-Value Observed: 0.206 (Depositor) 

Space Group: C 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 153.964	α = 90
b = 185.844	β = 90
c = 72.56	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-02-22 
Deposition Author(s): Geiger, J., Strom, S.

Revision History  

• Version 1.0: 2012-02-22
  Type: Initial release
  
• Version 1.1: 2012-11-14
  Changes: Database references
• Version 1.2: 2017-11-08
  Changes: Advisory, Refinement description
• Version 2.0: 2023-11-15
  Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations
• Version 2.1: 2026-03-18
  Changes: Derived calculations, Structure summary