6YAV | pdb_00006yav

Structure of FeSII (Shethna) protein from Azotobacter vinelandii

PDB DOI: https://doi.org/10.2210/pdb6YAV/pdb

Classification: METAL BINDING PROTEIN
Organism(s): Azotobacter vinelandii
Expression System: Escherichia coli KRX
Mutation(s): No

Deposited: 2020-03-13 Released: 2021-03-31
Deposition Author(s): Kabasakal, B.V., Kung, W.K.A., Cotton, C.A.R., Lieber, L., McFarlane, C.R., Murray, J.W.
Funding Organization(s): Biotechnology and Biological Sciences Research Council (BBSRC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.65 Å
R-Value Free:
0.225 (Depositor), 0.228 (DCC)
R-Value Work:
0.198 (Depositor), 0.201 (DCC)
R-Value Observed:
0.199 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

Structure of FeSII (Shethna) protein from Azotobacter vinelandii

Kabasakal, B.V., Kung, W.K.A., Cotton, C.A.R., Lieber, L., McFarlane, C.R., Murray, J.W.

To be published.

Macromolecule Content

Total Structure Weight: 67.53 kDa
Atom Count: 4,656
Modeled Residue Count: 585
Deposited Residue Count: 610
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dimeric (2Fe-2S) protein	A [auth E], B [auth A], C [auth B], D [auth C], E [auth D]	122	Azotobacter vinelandii	Mutation(s): 0
UniProt
Find proteins for Q44501 (Azotobacter vinelandii) Explore Q44501 Go to UniProtKB: Q44501
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q44501
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 F [auth E] SDF format, chain I [auth A] SDF format, chain J [auth B] SDF format, chain K [auth C] SDF format, chain L [auth D] MOL2 format, chain F [auth E] MOL2 format, chain I [auth A] MOL2 format, chain J [auth B] MOL2 format, chain K [auth C] MOL2 format, chain L [auth D] mmCIF format, chain F [auth E] mmCIF format, chain I [auth A] mmCIF format, chain J [auth B] mmCIF format, chain K [auth C] mmCIF format, chain L [auth D]	F [auth E], I [auth A], J [auth B], K [auth C], L [auth D]	FE2/S2 (INORGANIC) CLUSTER Fe₂ S₂ NIXDOXVAJZFRNF-UHFFFAOYSA-N		Interactions Focus chain F [auth E] Focus chain I [auth A] Focus chain J [auth B] Focus chain K [auth C] Focus chain L [auth D] Interactions & Density Focus chain F [auth E] Focus chain I [auth A] Focus chain J [auth B] Focus chain K [auth C] Focus chain L [auth D]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain G [auth E] SDF format, chain M [auth D] MOL2 format, chain G [auth E] MOL2 format, chain M [auth D] mmCIF format, chain G [auth E] mmCIF format, chain M [auth D]	G [auth E], M [auth D]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain G [auth E] Focus chain M [auth D] Interactions & Density Focus chain G [auth E] Focus chain M [auth D]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain H [auth E] MOL2 format, chain H [auth E] mmCIF format, chain H [auth E]	H [auth E]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain H [auth E] Interactions & Density Focus chain H [auth E]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.65 Å
R-Value Free: 0.225 (Depositor), 0.228 (DCC)
R-Value Work: 0.198 (Depositor), 0.201 (DCC)
R-Value Observed: 0.199 (Depositor)

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 134.24	α = 90
b = 135.1	β = 90
c = 37.09	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PHENIX	refinement
xia2	data reduction
xia2	data scaling
PHASER	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2021-03-31

Deposition Author(s):

Funding Organization	Location	Grant Number
Biotechnology and Biological Sciences Research Council (BBSRC)	United Kingdom	BB/L011468/1
Biotechnology and Biological Sciences Research Council (BBSRC)	United Kingdom	BB/J014575/1