3PDI

Precursor bound NifEN

PDB DOI: https://doi.org/10.2210/pdb3PDI/pdb

Classification: PROTEIN BINDING
Organism(s): Azotobacter vinelandii DJ
Expression System: Azotobacter vinelandii
Mutation(s): No

Deposited: 2010-10-22 Released: 2011-01-19
Deposition Author(s): Kaiser, J.T., Hu, Y., Wiig, J.A., Rees, D.C., Ribbe, M.W.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.341
R-Value Work: 0.294
R-Value Observed: 0.299

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Structure of Precursor-Bound NifEN: A Nitrogenase FeMo Cofactor Maturase/Insertase.

Kaiser, J.T., Hu, Y., Wiig, J.A., Rees, D.C., Ribbe, M.W.

(2011) Science 331: 91-94

PubMed: 21212358 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1126/science.1196954
Primary Citation of Related Structures:
3PDI

PubMed Abstract:
NifEN plays an essential role in the biosynthesis of the nitrogenase iron-molybdenum (FeMo) cofactor (M cluster). It is an α(2)β(2) tetramer that is homologous to the catalytic molybdenum-iron (MoFe) protein (NifDK) component of nitrogenase. NifEN serves as a scaffold for the conversion of an iron-only precursor to a matured form of the M cluster before delivering the latter to its target location within NifDK. Here, we present the structure of the precursor-bound NifEN of Azotobacter vinelandii at 2.6 angstrom resolution. From a structural comparison of NifEN with des-M-cluster NifDK and holo NifDK, we propose similar pathways of cluster insertion for the homologous NifEN and NifDK proteins.

Organizational Affiliation

Division of Chemistry and Chemical Engineering, California Institute of Technology, Mail Code 114-96, Pasadena, CA 91125, USA.

Macromolecule Content

Total Structure Weight: 413.77 kDa
Atom Count: 26,112
Modelled Residue Count: 3,436
Deposited Residue Count: 3,764
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nitrogenase MoFe cofactor biosynthesis protein NifE	A, C, E, G	483	Azotobacter vinelandii DJ	Mutation(s): 0 Gene Names: Avin_01450, nifE
UniProt
Find proteins for C1DH03 (Azotobacter vinelandii (strain DJ / ATCC BAA-1303)) Explore C1DH03 Go to UniProtKB: C1DH03
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	C1DH03
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Nitrogenase MoFe cofactor biosynthesis protein NifN	B, D, F, H	458	Azotobacter vinelandii DJ	Mutation(s): 0 Gene Names: Avin_01470, nifN
UniProt
Find proteins for C1DH04 (Azotobacter vinelandii (strain DJ / ATCC BAA-1303)) Explore C1DH04 Go to UniProtKB: C1DH04
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	C1DH04
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CZL Query on CZL Download Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain N [auth E] SDF format, chain P [auth G] SDF format, chain L [auth C] MOL2 format, chain J [auth A] MOL2 format, chain N [auth E] MOL2 format, chain P [auth G] MOL2 format, chain L [auth C] mmCIF format, chain J [auth A] mmCIF format, chain N [auth E] mmCIF format, chain P [auth G] mmCIF format, chain L [auth C]	J [auth A], L [auth C], N [auth E], P [auth G]	L-Cluster (Fe8S9) Fe₈ H₆ S₉ FRFZBLMXGBLMJN-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Focus chain L [auth C] Focus chain N [auth E] Focus chain P [auth G] Interactions & Density Focus chain J [auth A] Focus chain L [auth C] Focus chain N [auth E] Focus chain P [auth G]
SF4 Query on SF4 Download Ideal Coordinates CCD File SDF format, chain O [auth G] SDF format, chain I [auth A] SDF format, chain K [auth C] SDF format, chain M [auth E] MOL2 format, chain O [auth G] MOL2 format, chain I [auth A] MOL2 format, chain K [auth C] MOL2 format, chain M [auth E] mmCIF format, chain O [auth G] mmCIF format, chain I [auth A] mmCIF format, chain K [auth C] mmCIF format, chain M [auth E]	I [auth A], K [auth C], M [auth E], O [auth G]	IRON/SULFUR CLUSTER Fe₄ S₄ LJBDFODJNLIPKO-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain K [auth C] Focus chain M [auth E] Focus chain O [auth G] Interactions & Density Focus chain I [auth A] Focus chain K [auth C] Focus chain M [auth E] Focus chain O [auth G]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.341
R-Value Work: 0.294
R-Value Observed: 0.299
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 146.07	α = 90
b = 95.22	β = 95.5
c = 149.98	γ = 90

Software Package:

Software Name	Purpose
Blu-Ice	data collection
PHASER	phasing
PHENIX	refinement
XDS	data reduction
SCALA	data scaling

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2011-01-19

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2011-01-19
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2024-02-21
Changes: Data collection, Database references, Derived calculations