5EOW

Crystal Structure of 6-Hydroxynicotinic Acid 3-Monooxygenase from Pseudomonas putida KT2440

PDB DOI: https://doi.org/10.2210/pdb5EOW/pdb

Classification: OXIDOREDUCTASE
Organism(s): Pseudomonas putida KT2440
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2015-11-10 Released: 2016-06-08
Deposition Author(s): Yuen, M.E., Zhen, W., Gerwig, T.J., Story, R.W., Kopp, M., Nakamoto, K., Snider, M.J., Hicks, K.A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.253
R-Value Work: 0.206
R-Value Observed: 0.210

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Structural and Biochemical Characterization of 6-Hydroxynicotinic Acid 3-Monooxygenase, A Novel Decarboxylative Hydroxylase Involved in Aerobic Nicotinate Degradation.

Hicks, K.A., Yuen, M.E., Zhen, W.F., Gerwig, T.J., Story, R.W., Kopp, M.C., Snider, M.J.

(2016) Biochemistry 55: 3432-3446

PubMed: 27218267 Search on PubMed
DOI: https://doi.org/10.1021/acs.biochem.6b00105
Primary Citation of Related Structures:
5EOW

Organizational Affiliation

Department of Chemistry, SUNY Cortland , Cortland, New York 13045, United States.

Macromolecule Content

Total Structure Weight: 46.78 kDa
Atom Count: 2,828
Modelled Residue Count: 353
Deposited Residue Count: 405
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
6-hydroxynicotinate 3-monooxygenase	A	405	Pseudomonas putida KT2440	Mutation(s): 0 Gene Names: nicC, PP_3944 EC: 1.14.13.114
UniProt
Find proteins for Q88FY2 (Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440)) Explore Q88FY2 Go to UniProtKB: Q88FY2
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q88FY2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 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]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.253
R-Value Work: 0.206
R-Value Observed: 0.210
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.694	α = 90
b = 69.469	β = 90
c = 115.429	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
HKL-2000	data scaling
AutoSol	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2016-06-08

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2016-06-08
Type: Initial release
Version 1.1: 2016-07-06
Changes: Database references
Version 1.2: 2024-10-16
Changes: Data collection, Database references, Derived calculations, Structure summary