4UTJ

XenA - oxidized - Y183F variant in complex with 8-hydroxycoumarin

PDB DOI: https://doi.org/10.2210/pdb4UTJ/pdb

Classification: OXIDOREDUCTASE
Organism(s): Pseudomonas putida
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2014-07-21 Released: 2015-08-05
Deposition Author(s): Werther, T., Dobbek, H.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.07 Å
R-Value Free: 0.140
R-Value Work: 0.125
R-Value Observed: 0.125

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.0 of the entry. See complete history.

Literature

Redox-dependent substrate-cofactor interactions in the Michaelis-complex of a flavin-dependent oxidoreductase

Werther, T., Wahlefeld, S., Salewski, J., Kuhlmann, U., Zebger, I., Hildebrandt, P., Dobbek, H.

(2017) Nat Commun 8: 16084

DOI: https://doi.org/10.1038/ncomms16084

Macromolecule Content

Total Structure Weight: 41 kDa
Atom Count: 3,523
Modelled Residue Count: 360
Deposited Residue Count: 365
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH:flavin oxidoreductase	A	365	Pseudomonas putida	Mutation(s): 1 Gene Names: B7H19_27640
UniProt
Find proteins for Q3ZDM6 (Pseudomonas putida) Explore Q3ZDM6 Go to UniProtKB: Q3ZDM6
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q3ZDM6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FMN Query on FMN Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	B [auth A]	FLAVIN MONONUCLEOTIDE C₁₇ H₂₁ N₄ O₉ P FVTCRASFADXXNN-SCRDCRAPSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
8CM Query on 8CM Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A]	C [auth A]	8-HYDROXYCOUMARIN C₉ H₆ O₃ DPTUTXWBBUARQB-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A]	D [auth A], E [auth A], F [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.07 Å
R-Value Free: 0.140
R-Value Work: 0.125
R-Value Observed: 0.125
Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.98	α = 90
b = 83.36	β = 90
c = 156.36	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2015-08-05

Deposition Author(s):

Werther, T.

Dobbek, H.

Revision History (Full details and data files)

Version 1.0: 2015-08-05
Type: Initial release
Version 1.1: 2017-08-16
Changes: Database references
Version 2.0: 2017-08-23
Changes: Atomic model, Database references, Source and taxonomy, Structure summary

Prepare Data

Validate Data

Deposit Data

Help and Resources

4UTJ

XenA - oxidized - Y183F variant in complex with 8-hydroxycoumarin

Redox-dependent substrate-cofactor interactions in the Michaelis-complex of a flavin-dependent oxidoreductase

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

Expand

Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)