7BUH | pdb_00007buh

Reduced ferredoxin of carbazole 1,9a-dioxygenase

PDB DOI: https://doi.org/10.2210/pdb7BUH/pdb

Classification: OXIDOREDUCTASE
Organism(s): Metapseudomonas resinovorans
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2020-04-06 Released: 2021-04-07
Deposition Author(s): Matsuzawa, J., Wang, Y.X., Suzuki-Minakuchi, C., Nojiri, H.
Funding Organization(s): Noda Institute for Scientific Research

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.79 Å
R-Value Free:
0.201 (Depositor), 0.211 (DCC)
R-Value Work:
0.157 (Depositor), 0.168 (DCC)
R-Value Observed:
0.159 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

Reduced ferredoxin of carbazole 1,9a-dioxygenase

Matsuzawa, J., Wang, Y.X., Suzuki-Minakuchi, C., Nojiri, H.

To be published.

Macromolecule Content

Total Structure Weight: 12.71 kDa
Atom Count: 979
Modeled Residue Count: 113
Deposited Residue Count: 115
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ferredoxin CarAc	A	115	Metapseudomonas resinovorans	Mutation(s): 0 Gene Names: carAc
UniProt
Find proteins for Q8GI16 (Metapseudomonas resinovorans) Explore Q8GI16 Go to UniProtKB: Q8GI16
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8GI16
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FES (Subject of Investigation/LOI) Query on FES Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	FE2/S2 (INORGANIC) CLUSTER Fe₂ S₂ NIXDOXVAJZFRNF-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.79 Å
R-Value Free: 0.201 (Depositor), 0.211 (DCC)
R-Value Work: 0.157 (Depositor), 0.168 (DCC)
R-Value Observed: 0.159 (Depositor)

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.045	α = 90
b = 67.725	β = 90
c = 45.45	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
iMOSFLM	data reduction
Aimless	data scaling
MOLREP	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2021-04-07

Deposition Author(s):

Suzuki-Minakuchi, C.

Funding Organization	Location	Grant Number
Noda Institute for Scientific Research	Japan	--

Revision History (Full details and data files)

Version 1.0: 2021-04-07
Type: Initial release
Version 1.1: 2023-11-29
Changes: Data collection, Database references, Refinement description

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.