2W0Q | pdb_00002w0q

E. coli copper amine oxidase in complex with Xenon

PDB DOI: https://doi.org/10.2210/pdb2W0Q/pdb

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

Deposited: 2008-08-20 Released: 2008-12-16
Deposition Author(s): Pirrat, P., Smith, M.A., Pearson, A.R., McPherson, M.J., Phillips, S.E.V.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.48 Å
R-Value Free:
0.219 (Depositor), 0.220 (DCC)
R-Value Work:
0.158 (Depositor), 0.159 (DCC)
R-Value Observed:
0.161 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

Structure of a Xenon Derivative of Escherichia Coli Copper Amine Oxidase: Confirmation of the Proposed Oxygen-Entry Pathway.

Pirrat, P., Smith, M.A., Pearson, A.R., McPherson, M.J., Phillips, S.E.V.

(2008) Acta Crystallogr Sect F Struct Biol Cryst Commun 64: 1105

PubMed: 19052360 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1107/S1744309108036373
Primary Citation Related Structures:
2W0Q

PubMed Abstract:
The mechanism of molecular oxygen entry into the buried active site of the copper amine oxidase family has been investigated in several family members using biochemical, structural and in silico methods. These studies have revealed a structurally conserved beta-sandwich which acts as a hydrophobic reservoir from which molecular oxygen can take several species-specific preferred pathways to the active site. Escherichia coli copper amine oxidase (ECAO) possesses an extra N-terminal domain that lies close to one entrance to the beta-sandwich. In order to investigate whether the presence of this domain alters molecular oxygen entry in this enzyme, xenon was used as a molecular oxygen binding-site probe. The resulting 2.5 A resolution X-ray crystal structure reveals xenon bound in similar positions to those observed in xenon-derivative crystal structures of other family members, suggesting that the N-terminal domain does not affect oxygen entry and that the E. coli enzyme takes up oxygen in a similar manner to the rest of the copper amine oxidase family.

Organizational Affiliation

Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, England.

Macromolecule Content

Total Structure Weight: 164.47 kDa
Atom Count: 11,947
Modeled Residue Count: 1,440
Deposited Residue Count: 1,454
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
COPPER AMINE OXIDASE	A, B	727	Escherichia coli	Mutation(s): 0 EC: 1.4.3.4 (PDB Primary Data), 1.4.3.21 (UniProt)
UniProt
Find proteins for P46883 (Escherichia coli (strain K12)) Explore P46883 Go to UniProtKB: P46883
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P46883
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
XE Query on XE Download:Ideal Coordinates CCD File SDF format, chain S [auth B] SDF format, chain R [auth B] SDF format, chain Q [auth B] SDF format, chain P [auth B] SDF format, chain O [auth B] SDF format, chain K [auth A] SDF format, chain J [auth A] SDF format, chain I [auth A] SDF format, chain H [auth A] SDF format, chain G [auth A] SDF format, chain F [auth A] MOL2 format, chain S [auth B] MOL2 format, chain R [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain P [auth B] MOL2 format, chain O [auth B] MOL2 format, chain K [auth A] MOL2 format, chain J [auth A] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] mmCIF format, chain S [auth B] mmCIF format, chain R [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain P [auth B] mmCIF format, chain O [auth B] mmCIF format, chain K [auth A] mmCIF format, chain J [auth A] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A]	F [auth A] G [auth A] H [auth A] I [auth A] J [auth A] F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], O [auth B], P [auth B], Q [auth B], R [auth B], S [auth B]	XENON Xe FHNFHKCVQCLJFQ-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B]
CU Query on CU Download:Ideal Coordinates CCD File SDF format, chain L [auth B] SDF format, chain C [auth A] MOL2 format, chain L [auth B] MOL2 format, chain C [auth A] mmCIF format, chain L [auth B] mmCIF format, chain C [auth A]	C [auth A], L [auth B]	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain L [auth B] Interactions & Density Focus chain C [auth A] Focus chain L [auth B]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain N [auth B] SDF format, chain M [auth B] SDF format, chain E [auth A] SDF format, chain D [auth A] MOL2 format, chain N [auth B] MOL2 format, chain M [auth B] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] mmCIF format, chain N [auth B] mmCIF format, chain M [auth B] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A]	D [auth A], E [auth A], M [auth B], N [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain M [auth B] Focus chain N [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain M [auth B] Focus chain N [auth B]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
TPQ Query on TPQ	A, B	L-PEPTIDE LINKING	C₉ H₉ N O₅		TYR

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.48 Å
R-Value Free: 0.219 (Depositor), 0.220 (DCC)
R-Value Work: 0.158 (Depositor), 0.159 (DCC)
R-Value Observed: 0.161 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 134.588	α = 90
b = 166.871	β = 90
c = 80.33	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

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Entry History

Deposition Data

Released Date: 2008-12-16

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2008-12-16
Type: Initial release
Version 1.1: 2011-05-08
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2025-04-09
Changes: Data collection, Database references, Derived calculations, Other, Structure summary

2W0Q | pdb_00002w0q

E. coli copper amine oxidase in complex with Xenon

Literature

Structure of a Xenon Derivative of Escherichia Coli Copper Amine Oxidase: Confirmation of the Proposed Oxygen-Entry Pathway.

Biological Assembly 1

Macromolecules

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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