2FZN | pdb_00002fzn

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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.251 (Depositor), 0.262 (DCC)
R-Value Work:
0.214 (Depositor), 0.222 (DCC)
R-Value Observed:
0.216 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

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.

Macromolecule Content

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

Macromolecules

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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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P09546
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FAD Query on FAD Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	FLAVIN-ADENINE DINUCLEOTIDE C₂₇ H₃₃ N₉ O₁₅ P₂ VWWQXMAJTJZDQX-UYBVJOGSSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
PRO Query on PRO Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	PROLINE C₅ H₉ N O₂ ONIBWKKTOPOVIA-BYPYZUCNSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.251 (Depositor), 0.262 (DCC)
R-Value Work: 0.214 (Depositor), 0.222 (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

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Entry History

Deposition Data

Released Date: 2006-12-26

Deposition Author(s):

Revision History (Full details and data files)

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

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.