7QQA | pdb_00007qqa

MgADP-bound Fe protein of the iron-only nitrogenase from Azotobacter vinelandii

PDB DOI: https://doi.org/10.2210/pdb7QQA/pdb

Classification: ELECTRON TRANSPORT
Organism(s): Azotobacter vinelandii
Mutation(s): No

Deposited: 2022-01-07 Released: 2022-06-22
Deposition Author(s): Trncik, C., Mueller, T., Franke, P., Einsle, O.
Funding Organization(s): German Research Foundation (DFG), European Research Council (ERC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.79 Å
R-Value Free:
0.249 (Depositor), 0.250 (DCC)
R-Value Work:
0.197 (Depositor), 0.202 (DCC)
R-Value Observed:
0.200 (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

MgADP-bound Fe protein of the iron-only nitrogenase from Azotobacter vinelandii

Trncik, C., Mueller, T., Franke, P., Einsle, O.

(2022) Journal Of Inorganic Biochemistry 227

Macromolecule Content

Total Structure Weight: 122.35 kDa
Atom Count: 9,212
Modeled Residue Count: 1,088
Deposited Residue Count: 1,096
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nitrogenase iron protein	A, B, C, D	274	Azotobacter vinelandii	Mutation(s): 0 EC: 1.18.6.1
UniProt
Find proteins for C1DK95 (Azotobacter vinelandii (strain DJ / ATCC BAA-1303)) Explore C1DK95 Go to UniProtKB: C1DK95
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	C1DK95
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ADP Query on ADP Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain H [auth B] SDF format, chain M [auth D] SDF format, chain J [auth C] MOL2 format, chain E [auth A] MOL2 format, chain H [auth B] MOL2 format, chain M [auth D] MOL2 format, chain J [auth C] mmCIF format, chain E [auth A] mmCIF format, chain H [auth B] mmCIF format, chain M [auth D] mmCIF format, chain J [auth C]	E [auth A], H [auth B], J [auth C], M [auth D]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain E [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain M [auth D] Interactions & Density Focus chain E [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain M [auth D]
SF4 (Subject of Investigation/LOI) Query on SF4 Download:Ideal Coordinates CCD File SDF format, chain L [auth C] SDF format, chain G [auth A] MOL2 format, chain L [auth C] MOL2 format, chain G [auth A] mmCIF format, chain L [auth C] mmCIF format, chain G [auth A]	G [auth A], L [auth C]	IRON/SULFUR CLUSTER Fe₄ S₄ LJBDFODJNLIPKO-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain L [auth C] Interactions & Density Focus chain G [auth A] Focus chain L [auth C]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain I [auth B] SDF format, chain N [auth D] SDF format, chain K [auth C] MOL2 format, chain F [auth A] MOL2 format, chain I [auth B] MOL2 format, chain N [auth D] MOL2 format, chain K [auth C] mmCIF format, chain F [auth A] mmCIF format, chain I [auth B] mmCIF format, chain N [auth D] mmCIF format, chain K [auth C]	F [auth A], I [auth B], K [auth C], N [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain I [auth B] Focus chain K [auth C] Focus chain N [auth D] Interactions & Density Focus chain F [auth A] Focus chain I [auth B] Focus chain K [auth C] Focus chain N [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.79 Å
R-Value Free: 0.249 (Depositor), 0.250 (DCC)
R-Value Work: 0.197 (Depositor), 0.202 (DCC)
R-Value Observed: 0.200 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.677	α = 68.57
b = 80.366	β = 75.85
c = 80.024	γ = 76.03

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
autoPROC	data scaling
MOLREP	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2022-06-22

Deposition Author(s):

Funding Organization	Location	Grant Number
German Research Foundation (DFG)	European Union	235777276
German Research Foundation (DFG)	European Union	273919336
European Research Council (ERC)	European Union	310656