1O7M | pdb_00001o7m

NAPHTHALENE 1,2-DIOXYGENASE, BINARY COMPLEX WITH DIOXYGEN

PDB DOI: https://doi.org/10.2210/pdb1O7M/pdb

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

Deposited: 2002-11-11 Released: 2003-02-20
Deposition Author(s): Karlsson, A., Parales, J.V., Parales, R.E., Gibson, D.T., Eklund, H., Ramaswamy, S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.75 Å
R-Value Free:
0.187 (Depositor), 0.194 (DCC)
R-Value Work:
0.178 (Depositor), 0.190 (DCC)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

Crystal Structure of Naphthalene Dioxygenase: Side-on Binding of Dioxygen to Iron

Karlsson, A., Parales, J.V., Parales, R.E., Gibson, D.T., Eklund, H., Ramaswamy, S.

(2003) Science 299: 1039

PubMed: 12586937 Search on PubMed
DOI: https://doi.org/10.1126/science.1078020
Primary Citation Related Structures:
1O7G, 1O7H, 1O7M, 1O7N, 1O7P, 1O7W

PubMed Abstract:
Binding of oxygen to iron is exploited in several biological and chemical processes. Although computational and spectroscopic results have suggested side-on binding, only end-on binding of oxygen to iron has been observed in crystal structures. We have determined structures of naphthalene dioxygenase that show a molecular oxygen species bound to the mononuclear iron in a side-on fashion. In a complex with substrate and dioxygen, the dioxygen molecule is lined up for an attack on the double bond of the aromatic substrate. The structures reported here provide the basis for a reaction mechanism and for the high stereospecificity of the reaction catalyzed by naphthalene dioxygenase.

Organizational Affiliation

Department of Molecular Biology, Swedish University of Agricultural Sciences, Box 590, Biomedical Center, 75124 Uppsala, Sweden.

Macromolecule Content

Total Structure Weight: 73.56 kDa
Atom Count: 5,694
Modeled Residue Count: 641
Deposited Residue Count: 643
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NAPHTHALENE 1,2-DIOXYGENASE ALPHA SUBUNIT	A	449	Pseudomonas putida	Mutation(s): 0 EC: 1.14.12.12
UniProt
Find proteins for P0A110 (Pseudomonas putida) Explore P0A110 Go to UniProtKB: P0A110
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0A110
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
NAPHTHALENE 1,2-DIOXYGENASE BETA SUBUNIT	B	194	Pseudomonas putida	Mutation(s): 0 EC: 1.14.12.12
UniProt
Find proteins for P0A112 (Pseudomonas putida) Explore P0A112 Go to UniProtKB: P0A112
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0A112
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FES Query on FES Download:Ideal Coordinates CCD File SDF format, chain H [auth A] MOL2 format, chain H [auth A] mmCIF format, chain H [auth A]	H [auth A]	FE2/S2 (INORGANIC) CLUSTER Fe₂ S₂ NIXDOXVAJZFRNF-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Interactions & Density Focus chain H [auth A]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain L [auth B] SDF format, chain M [auth B] MOL2 format, chain G [auth A] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] mmCIF format, chain G [auth A] mmCIF format, chain L [auth B] mmCIF format, chain M [auth B]	G [auth A], L [auth B], M [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain G [auth A] Focus chain L [auth B] Focus chain M [auth B] Interactions & Density Focus chain G [auth A] Focus chain L [auth B] Focus chain M [auth B]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain J [auth B] SDF format, chain K [auth B] SDF format, chain N [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B] MOL2 format, chain N [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain J [auth B] mmCIF format, chain K [auth B] mmCIF format, chain N [auth B]	C [auth A] D [auth A] E [auth A] J [auth B] K [auth B] C [auth A], D [auth A], E [auth A], J [auth B], K [auth B], N [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain N [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain N [auth B]
FE Query on FE Download:Ideal Coordinates CCD File SDF format, chain I [auth A] MOL2 format, chain I [auth A] mmCIF format, chain I [auth A]	I [auth A]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Interactions & Density Focus chain I [auth A]
OXY Query on OXY Download:Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	F [auth A]	OXYGEN MOLECULE O₂ MYMOFIZGZYHOMD-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.75 Å
R-Value Free: 0.187 (Depositor), 0.194 (DCC)
R-Value Work: 0.178 (Depositor), 0.190 (DCC)

Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 140.277	α = 90
b = 140.277	β = 90
c = 208.754	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
d*TREK	data reduction
d*TREK	data scaling

Structure Validation

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Entry History

Deposition Data

Released Date: 2003-02-20

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2003-02-20
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: 2017-07-05
Changes: Data collection
Version 1.4: 2023-12-13
Changes: Data collection, Database references, Derived calculations, Other, Refinement description