3GKQ | pdb_00003gkq

Terminal oxygenase of carbazole 1,9a-dioxygenase from Novosphingobium sp. KA1

PDB DOI: https://doi.org/10.2210/pdb3GKQ/pdb

Classification: OXIDOREDUCTASE
Organism(s): Novosphingobium sp. KA1
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2009-03-11 Released: 2010-03-31
Deposition Author(s): Umeda, T., Nojiri, H.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free:
0.436 (Depositor), 0.199 (DCC)
R-Value Work:
0.201 (Depositor), 0.197 (DCC)
R-Value Observed:
0.214 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

Specific interaction via putidaredoxin-type ferredoxin in carbazole 1,9a-dioxygenase from Novosphingobium sp. KA1

Umeda, T., Katsuki, J., Ashikawa, Y., Inoue, K., Usami, Y., Noguchi, H., Terada, T., Abo, M., Fujimoto, Z., Yamane, H., Nojiri, H.

To be published.

Macromolecule Content

Total Structure Weight: 265.71 kDa
Atom Count: 20,106
Modeled Residue Count: 2,241
Deposited Residue Count: 2,334
Unique protein chains: 1

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Terminal oxygenase component of carbazole 1,9a-dioxygenase	A, B, C, D, E A, B, C, D, E, F	389	Novosphingobium sp. KA1	Mutation(s): 0 Gene Names: carAaII
UniProt
Find proteins for Q2PFA6 (Novosphingobium sp. (strain KA1)) Explore Q2PFA6 Go to UniProtKB: Q2PFA6
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q2PFA6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FES Query on FES Download:Ideal Coordinates CCD File SDF format, chain K [auth B] SDF format, chain N [auth C] SDF format, chain Q [auth D] SDF format, chain T [auth E] SDF format, chain W [auth F] SDF format, chain H [auth A] MOL2 format, chain K [auth B] MOL2 format, chain N [auth C] MOL2 format, chain Q [auth D] MOL2 format, chain T [auth E] MOL2 format, chain W [auth F] MOL2 format, chain H [auth A] mmCIF format, chain K [auth B] mmCIF format, chain N [auth C] mmCIF format, chain Q [auth D] mmCIF format, chain T [auth E] mmCIF format, chain W [auth F] mmCIF format, chain H [auth A]	H [auth A] K [auth B] N [auth C] Q [auth D] T [auth E] H [auth A], K [auth B], N [auth C], Q [auth D], T [auth E], W [auth F]	FE2/S2 (INORGANIC) CLUSTER Fe₂ S₂ NIXDOXVAJZFRNF-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain K [auth B] Focus chain N [auth C] Focus chain Q [auth D] Focus chain T [auth E] Focus chain W [auth F] Interactions & Density Focus chain H [auth A] Focus chain K [auth B] Focus chain N [auth C] Focus chain Q [auth D] Focus chain T [auth E] Focus chain W [auth F]
FE2 Query on FE2 Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain I [auth A] SDF format, chain J [auth B] SDF format, chain L [auth B] SDF format, chain M [auth C] SDF format, chain O [auth C] SDF format, chain S [auth E] SDF format, chain U [auth E] SDF format, chain V [auth F] SDF format, chain X [auth F] SDF format, chain R [auth D] SDF format, chain P [auth D] MOL2 format, chain G [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth B] MOL2 format, chain L [auth B] MOL2 format, chain M [auth C] MOL2 format, chain O [auth C] MOL2 format, chain S [auth E] MOL2 format, chain U [auth E] MOL2 format, chain V [auth F] MOL2 format, chain X [auth F] MOL2 format, chain R [auth D] MOL2 format, chain P [auth D] mmCIF format, chain G [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth B] mmCIF format, chain L [auth B] mmCIF format, chain M [auth C] mmCIF format, chain O [auth C] mmCIF format, chain S [auth E] mmCIF format, chain U [auth E] mmCIF format, chain V [auth F] mmCIF format, chain X [auth F] mmCIF format, chain R [auth D] mmCIF format, chain P [auth D]	G [auth A] I [auth A] J [auth B] L [auth B] M [auth C] G [auth A], I [auth A], J [auth B], L [auth B], M [auth C], O [auth C], P [auth D], R [auth D], S [auth E], U [auth E], V [auth F], X [auth F]	FE (II) ION Fe CWYNVVGOOAEACU-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain I [auth A] Focus chain J [auth B] Focus chain L [auth B] Focus chain M [auth C] Focus chain O [auth C] Focus chain P [auth D] Focus chain R [auth D] Focus chain S [auth E] Focus chain U [auth E] Focus chain V [auth F] Focus chain X [auth F] Interactions & Density Focus chain G [auth A] Focus chain I [auth A] Focus chain J [auth B] Focus chain L [auth B] Focus chain M [auth C] Focus chain O [auth C] Focus chain P [auth D] Focus chain R [auth D] Focus chain S [auth E] Focus chain U [auth E] Focus chain V [auth F] Focus chain X [auth F]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.436 (Depositor), 0.199 (DCC)
R-Value Work: 0.201 (Depositor), 0.197 (DCC)
R-Value Observed: 0.214 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 117.147	α = 90
b = 159.019	β = 94.45
c = 167.774	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
MOLREP	phasing
CNS	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2010-03-31

Deposition Author(s):

Umeda, T.

Nojiri, H.

Revision History (Full details and data files)

Version 1.0: 2010-03-31
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2015-04-08
Changes: Refinement description
Version 1.3: 2024-03-20
Changes: Data collection, Database references, Derived calculations
Version 1.4: 2026-08-12
Type: Remediation
Reason: Metalloprotein remediation
Changes: Derived calculations, Structure summary