2FZN

Structure of the E. coli PutA proline dehydrogenase domain reduced by dithionite and complexed with proline

• PDB DOI: https://doi.org/10.2210/pdb2FZN/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Escherichia coli
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2006-02-09 Released: 2006-12-26 
• Deposition Author(s): Tanner, J.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.251 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.214 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.216 (Depositor) 

Starting Model: experimental

Literature

Hydrogen Bonding Interactions of the 2-OH Ribityl Group and the N(5) Position of the FAD Cofactor Regulate PutA-membrane Associations in Escherichia coli

Zhang, W., Zhang, M., Zhu, W., Wanduragula, S., Rewinkel, D., Tanner, J.J., Becker, D.F.

To be published.

Biological Assembly 1  

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

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 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 67.57 kDa 
• Atom Count: 3,704 
• Modelled Residue Count: 449 
• Deposited Residue Count: 602 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bifunctional protein putA, Proline dehydrogenase (EC 1.5.99.8) (Proline oxidase)	A	602	Escherichia coli	Mutation(s): 0  Gene Names: putA EC: 1.5.99.8 (PDB Primary Data), 1.2.1.88 (UniProt), 1.5.5.2 (UniProt)
UniProt
Find proteins for P09546 (Escherichia coli (strain K12)) Explore P09546  Go to UniProtKB:  P09546

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FAD	B [auth A]	FLAVIN-ADENINE DINUCLEOTIDE C27 H33 N9 O15 P2 VWWQXMAJTJZDQX-UYBVJOGSSA-N
PRO	C [auth A]	PROLINE C5 H9 N O2 ONIBWKKTOPOVIA-BYPYZUCNSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.251 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.214 (Depositor), 0.220 (DCC) 
• R-Value Observed: 0.216 (Depositor) 

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.115	α = 90
b = 143.221	β = 90
c = 145.124	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-12-26 
Deposition Author(s): Tanner, J.J.

Revision History  

• Version 1.0: 2006-12-26
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.3: 2017-10-18
  Changes: Refinement description
• Version 1.4: 2023-08-30
  Changes: Data collection, Database references, Derived calculations, Refinement description