4HM1 | pdb_00004hm1

Naphthalene 1,2-Dioxygenase bound to 1-indanone

PDB DOI: https://doi.org/10.2210/pdb4HM1/pdb

Classification: Oxidoreductase/Oxidoreductase inhibitor
Organism(s): Pseudomonas sp. C18
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2012-10-17 Released: 2013-10-30
Deposition Author(s): Ferraro, D.J., Ramaswamy, S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free:
0.190 (Depositor), 0.188 (DCC)
R-Value Work:
0.149 (Depositor), 0.146 (DCC)
R-Value Observed:
0.151 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Naphthalene 1,2-Dioxygenase bound to 1-indanone

Ferraro, D.J., Ramaswamy, S.

To be published.

Macromolecule Content

Total Structure Weight: 73.88 kDa
Atom Count: 6,071
Modeled Residue Count: 638
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 subunit alpha	A	449	Pseudomonas sp. C18	Mutation(s): 0 Gene Names: doxB, NC_004999.1 EC: 1.14.12.12
UniProt
Find proteins for P0A111 (Pseudomonas sp. (strain C18)) Explore P0A111 Go to UniProtKB: P0A111
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0A111
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 subunit beta	B	194	Pseudomonas sp. C18	Mutation(s): 0 Gene Names: doxD, NC_004999.1 EC: 1.14.12.12
UniProt
Find proteins for P0A113 (Pseudomonas sp. (strain C18)) Explore P0A113 Go to UniProtKB: P0A113
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0A113
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 F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	F [auth A]	FE2/S2 (INORGANIC) CLUSTER Fe₂ S₂ NIXDOXVAJZFRNF-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]
1ON Query on 1ON 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]	2,3-dihydro-1H-inden-1-one C₉ H₈ O QNXSIUBBGPHDDE-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 P [auth B] SDF format, chain O [auth B] SDF format, chain K [auth A] SDF format, chain E [auth A] MOL2 format, chain P [auth B] MOL2 format, chain O [auth B] MOL2 format, chain K [auth A] MOL2 format, chain E [auth A] mmCIF format, chain P [auth B] mmCIF format, chain O [auth B] mmCIF format, chain K [auth A] mmCIF format, chain E [auth A]	E [auth A], K [auth A], O [auth B], P [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain E [auth A] Focus chain K [auth A] Focus chain O [auth B] Focus chain P [auth B] Interactions & Density Focus chain E [auth A] Focus chain K [auth A] Focus chain O [auth B] Focus chain P [auth B]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain M [auth B] SDF format, chain N [auth B] SDF format, chain Q [auth B] SDF format, chain L [auth B] SDF format, chain J [auth A] SDF format, chain I [auth A] SDF format, chain D [auth A] SDF format, chain C [auth A] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain L [auth B] MOL2 format, chain J [auth A] MOL2 format, chain I [auth A] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] mmCIF format, chain M [auth B] mmCIF format, chain N [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain L [auth B] mmCIF format, chain J [auth A] mmCIF format, chain I [auth A] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A]	C [auth A] D [auth A] I [auth A] J [auth A] L [auth B] C [auth A], D [auth A], I [auth A], J [auth A], L [auth B], M [auth B], N [auth B], Q [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain Q [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain Q [auth B]
FE Query on FE Download:Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A] mmCIF format, chain G [auth A]	G [auth A]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free: 0.190 (Depositor), 0.188 (DCC)
R-Value Work: 0.149 (Depositor), 0.146 (DCC)
R-Value Observed: 0.151 (Depositor)

Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 139.935	α = 90
b = 139.935	β = 90
c = 208.238	γ = 120

Software Package:

Software Name	Purpose
d*TREK	data reduction
PHENIX	refinement
PDB_EXTRACT	data extraction
d*TREK	data scaling
AMoRE	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2013-10-30

Deposition Author(s):

Ferraro, D.J.

Ramaswamy, S.

Revision History (Full details and data files)

Version 1.0: 2013-10-30
Type: Initial release
Version 1.1: 2024-11-06
Changes: Data collection, Database references, Derived calculations, Structure summary