5BOK | pdb_00005bok

Ferredoxin component of 3-nitrotoluene dioxygenase from Diaphorobacter sp. strain DS2

PDB DOI: https://doi.org/10.2210/pdb5BOK/pdb

Classification: METAL BINDING PROTEIN
Organism(s): Diaphorobacter sp. DS2
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2015-05-27 Released: 2016-07-27
Deposition Author(s): Ramaswamy, S., Kumari, A., Singh, D., Gurunath, R.
Funding Organization(s): Department of biotechnology

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free:
0.262 (Depositor), 0.261 (DCC)
R-Value Work:
0.231 (Depositor), 0.234 (DCC)
R-Value Observed:
0.233 (Depositor)

Starting Model: experimental
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This is version 1.1 of the entry. See complete history.

Literature

Ferredoxin component of 3-nitrotoluene dioxygenase from Diaphorobacter sp. strain DS2

Ramaswamy, S., Kumari, A., Singh, D., Qurunath, R.

To be published.

Macromolecule Content

Total Structure Weight: 11.72 kDa
Atom Count: 816
Modeled Residue Count: 102
Deposited Residue Count: 104
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ferredoxin	A	104	Diaphorobacter sp. DS2	Mutation(s): 0 Gene Names: mntAb
UniProt
Find proteins for A0ACD6B8N8 (Diaphorobacter sp. DS2) Explore A0ACD6B8N8 Go to UniProtKB: A0ACD6B8N8
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0ACD6B8N8
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 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]
FE Query on FE 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]	FE (III) ION Fe VTLYFUHAOXGGBS-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: 2.40 Å
R-Value Free: 0.262 (Depositor), 0.261 (DCC)
R-Value Work: 0.231 (Depositor), 0.234 (DCC)
R-Value Observed: 0.233 (Depositor)

Space Group: I 4 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79.53	α = 90
b = 79.53	β = 90
c = 108.97	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
MOSFLM	data reduction
SCALA	data scaling
d*TREK	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2016-07-27

Deposition Author(s):

Funding Organization	Location	Grant Number
Department of biotechnology	India	--

Revision History (Full details and data files)

Version 1.0: 2016-07-27
Type: Initial release
Version 1.1: 2023-11-08
Changes: Data collection, Database references, Derived calculations, 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.